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GitLab

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<h3>

Nilesh Patra pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/75edcfd0e34420503fdaf9924469fc19365da1fd">75edcfd0</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-03T01:24:05+05:30</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/21f321c993981370b0212e849993af7b2d2bdded">21f321c9</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-03T01:24:12+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.98.4+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/6785eb98e49bf441cd414306dd11a56cb7903146">6785eb98</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-03T01:26:04+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.98.4+dfsg'

Update to upstream version '0.98.4+dfsg'

with Debian dir f49962a5842ce7593c7eff0d268331d0f4929eb0</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/046486046166dd8ab3d08f9426bdd9a17ca9c8fd">04648604</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-03T01:28:59+05:30</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/gemma/-/commit/8cf6fd2b71c9510451401a4767f86ad116bfdc82">8cf6fd2b</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-02-03T01:29:26+05:30</i>

</div>

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

</pre>

</li>

</ul>

<h4>22 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#837f33c9bb9cda5fef808cd5015328088413ca74">

<span class="new-file">

+

.guix-dev-static

</span>

</a>

</li>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#b2270542d41297db1ee0d12698e609ea3ec25ce7">

INSTALL.md

</a>

</li>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">

RELEASE-NOTES.md

</a>

</li>

<li class="file-stats">

<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">

VERSION

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#f6361e25b2927c77444e8b661a216d7f56f9d1f8">

debian/patches/Makefile.patch

</a>

</li>

<li class="file-stats">

<a href="#26b6c1e1d4b838bcdd860d7c24ef8ef3b521d33f">

debian/patches/Reproducible_builds.patch

</a>

</li>

<li class="file-stats">

<a href="#4adf3f896c0b9b2ec23e956edfbf787c4ffec48c">

debian/patches/no-lquadmath.patch

</a>

</li>

<li class="file-stats">

<a href="#8799e0764d072adeaa173a1402f03a70ad62b5bd">

doc/manual.pdf

</a>

</li>

<li class="file-stats">

<a href="#708cbc7b584b2f8ebbf34725c60b059470cd4c33">

doc/manual.tex

</a>

</li>

<li class="file-stats">

<a href="#8830c9ed5fb31e949b61cb9b0e6e4a49f2d44d55">

<span class="new-file">

+

guix.scm

</span>

</a>

</li>

<li class="file-stats">

<a href="#7e010836fc66dfe28d372f4533ed86ba8aa18834">

src/gemma.cpp

</a>

</li>

<li class="file-stats">

<a href="#260f302861b2cad121d8bda95be454917dff6427">

src/gemma.h

</a>

</li>

<li class="file-stats">

<a href="#1b90beb6aa8a5b7cd88c6dee9504cb63db8a4c28">

src/lmm.cpp

</a>

</li>

<li class="file-stats">

<a href="#cf55255afff3a015e09fb646bb9473568ef880ef">

src/lmm.h

</a>

</li>

<li class="file-stats">

<a href="#d0b2a99ae59d4e70842a1e3d7c999a4769960f74">

src/param.cpp

</a>

</li>

<li class="file-stats">

<a href="#609cf42db3f9cb91789592673659daf4110a98e1">

src/param.h

</a>

</li>

<li class="file-stats">

<a href="#f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a">

src/version.h

</a>

</li>

<li class="file-stats">

<a href="#d8267812124820d08a2dfd506ddf2a9b9d0aefe9">

test/dev_test_suite.sh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="837f33c9bb9cda5fef808cd5015328088413ca74">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#837f33c9bb9cda5fef808cd5015328088413ca74"><strong>.guix-dev-static</strong></a>

<hr>

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

</td>

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

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Typical Guix container invocation</span>

</pre>

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

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

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="plaintext">~/opt/guix/bin/guix environment -C guix --ad-hoc gcc-toolchain:static gdb gsl openblas zlib:static bash ld-wrapper perl vim which gfortran-toolchain</span></pre>

</td>

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<br>

</li>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,8 @@ language: C++</td>

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

2

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

2

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

<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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

3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml">  <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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

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

4

</td>

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

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

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

</td>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml">      <span class="na" style="color: #008080;">arch</span><span class="pi">:</span></span>

</pre>

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

</td>

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

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">amd64</span></span>

</pre>

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

5

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

7

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml">      <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>

</pre>

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

6

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<td class="diff-line-num new_line" data-linenumber="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="yaml">      <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>

</pre>

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

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

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml">        <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>

</pre>

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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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,9 +23,21 @@ matrix:</td>

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

21

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

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">libopenblas-dev</span></span>

</pre>

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

22

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

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>

</pre>

</td>

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

23

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

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml">      <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>

</pre>

</td>

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

</td>

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

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="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="yaml">      <span class="na" style="color: #008080;">arch</span><span class="pi">:</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">arm64</span></span>

</pre>

</td>

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

</td>

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

29

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<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="yaml">      <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>

</pre>

</td>

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

</td>

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

30

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<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="yaml">      <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>

</pre>

</td>

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

</td>

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

31

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<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="yaml">        <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>

</pre>

</td>

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

</td>

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

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml">          <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>

</pre>

</td>

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

</td>

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

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml">          <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>

</pre>

</td>

</tr>

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

</td>

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

35

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">libgsl-dev</span></span>

</pre>

</td>

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

</td>

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

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">libopenblas-dev</span></span>

</pre>

</td>

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

24

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

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

</td>

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

25

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo $MATRIX_EVAL</span></span>

</pre>

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

26

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

39

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${MATRIX_EVAL}"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl ; fi</span></span>

</pre>

</td>

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

27

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

41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">$CXX --version</span></span>

</pre>

</td>

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

28

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<td class="diff-line-num 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">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl ; fi</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="diff-line-num new_line" data-linenumber="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="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then OPENBLAS="$(brew --prefix openblas)" ; fi</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="b2270542d41297db1ee0d12698e609ea3ec25ce7">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#b2270542d41297db1ee0d12698e609ea3ec25ce7"><strong>INSTALL.md</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">@@ -10,8 +10,8 @@ and it should give you the version.</td>

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

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

</pre>

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">GEMMA runs on Linux<span class="idiff left right"> and MAC OSX and the runtime has the following</span></span>

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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">GEMMA runs on Linux<span class="idiff left right">, MAC OSX and Windows (with Docker). The runtime</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="idiff left right">has the following </span>dependencies:</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">*</span> C++ tool chain >= 5.5.0 (see Travis CI and we test with file .guix-dev-gcc-older)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"><span class="p">*</span> GNU Science library (GSL) 2.x (GEMMA dropped support for GSL 1.x)</span>

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

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix package -i gemma</span></span>

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

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown">To build GEMMA from source you can opt to install the build tools with GNU Guix</span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">A more recent version may be found in the guix-bioinformatics channel</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown">which is maintained by the authors. See the</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">README</span><span class="p">](</span><span class="sx" style="color: #d14;">http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics</span><span class="p">)</span>, e.g.</span>

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

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <span class="idiff left right">guix package -i make gcc linux-libre-headers gsl openblas lapack glibc ld-wrapper</span></span></span>

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

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <span class="idiff left right">env GUIX_PACKAGE_PATH=./guix-bioinformatics guix package -A gemma</span></span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="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="markdown"></span>

</pre>

</td>

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

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">The current build container is in <span class="p">[</span><span class="nv" style="color: #008080;">guix-dev</span><span class="p">](</span><span class="sx" style="color: #d14;">../guix-dev</span><span class="p">)</span></span>

</pre>

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

</td>

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

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

<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">To build GEMMA from source you can opt to install the build tools with</span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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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="LC62" class="line" lang="markdown">GNU Guix, the current build container is in <span class="p">[</span><span class="nv" style="color: #008080;">guix-dev</span><span class="p">](</span><span class="sx" style="color: #d14;">./.guix-dev</span><span class="p">)</span></span>

</pre>

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

60

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

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

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

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim which</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="sb" style="color: #d14;">    source .guix-dev</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make</span></span>

</pre>

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

62

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); 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="markdown">To build with an older gcc, for example:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown">Guix allows for easy versioning. To build with an older gcc, for</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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

<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown">example:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="sb" style="color: #d14;">    guix environment -C guix --ad-hoc gcc-toolchain@9.3.0 gdb gsl openblas zlib bash ld-wrapper perl vim which</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC67" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Install from source</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Install with Docker</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown">Recent version of GEMMA come with a 64-bit Docker image that should run</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC75" class="line" lang="markdown">on Linux, Windows and MacOS.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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

<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

69

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<td class="diff-line-num new_line old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"><span class="idiff left right">Note: Eigen is no longer required!</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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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="LC77" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">### Install from source</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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

<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

71

</td>

<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown">Install listed dependencies and run</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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

<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">Install listed dependencies (you may want to take hints from</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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

<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">the Travis-CI <span class="p">[</span><span class="nv" style="color: #008080;">tests</span><span class="p">](</span><span class="sx" style="color: #d14;">./.travis.yml</span><span class="p">)</span>) and run</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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<td class="diff-line-num new_line" 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">

81

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

<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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

<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"><span class="sb" style="color: #d14;">      make -j 4</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

</td>

<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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

<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown">(the -j switch builds on 4 cores).</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

</td>

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

<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

77

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown">if you get an Eigen error you may need to override the include</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

78

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown">path. E.g. to build GEMMA on GNU Guix with shared libs the following</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

79

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC79" class="line" lang="markdown">may work</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

80

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

81

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

82

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

83

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown">another example overriding optimization and LIB flags (so as to link</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

84

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown">against gslv1) would be</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

85

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

86

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 WITH_OPENBLAS=1 GCC_FLAGS="-Wall" LIBS="$HOME/opt/gsl1/lib/libgsl.a $HOME/opt/gsl1/lib/libgslcblas.a -L$HOME/.guix-profile/lib -pthread -llapack -lblas -lz"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown">to run GEMMA tests</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="sb" style="color: #d14;">      time make check</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">You can run gemma in the debugger with, for example</span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -99,27 +95,23 @@ You can run gemma in the debugger with, for example</td>

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

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown">Note that if you get <span class="nt" style="color: #000080;"><optimized</span> <span class="na" style="color: #008080;">out</span><span class="nt" style="color: #000080;">></span> warnings on inspecting variables you</span>

</pre>

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown">should compile with GCC_FLAGS="" to disable optimizations (-O3). E.g.</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC102" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make <span class="idiff left right">EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 </span>WITH_OPENBLAS=1 GCC_FLAGS=</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make WITH_OPENBLAS=1 GCC_FLAGS=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown">Other options, such as compiling with warnings, are listed in the</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### GNU Guix commands used</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown">With git bisect build the older versions of gemma with openblas</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown">Some development examples.  With git bisect build the older versions</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown">of gemma with openblas</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

</td>

<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ~/.config/guix/current/bin/guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl <span class="idiff left right">eigen </span>lapack openblas zlib bash ld-wrapper perl ldc</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

112

</td>

<td class="diff-line-num new_line old" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make clean ; make <span class="idiff left right">EIGEN_INCLUDE_PATH=$GUIX_ENVIRONMENT/include/eigen3 </span>WITH_OPENBLAS=1 FORCE_DYNAMIC=1 -j 8</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

</td>

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

<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ~/.config/guix/current/bin/guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl lapack openblas zlib bash ld-wrapper perl ldc</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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

<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make clean ; make WITH_OPENBLAS=1 FORCE_DYNAMIC=1 -j 8</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

</td>

<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

</td>

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

<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>

</pre>

</td>

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

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

114

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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

<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown">or with atlas</span>

</pre>

</td>

</tr>

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

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

115

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

112

</td>

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

<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ~/.config/guix/current/bin/guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl eigen lapack atlas zlib bash ld-wrapper perl ldc</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

117

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC117" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make clean ; make EIGEN_INCLUDE_PATH=$GUIX_ENVIRONMENT/include/eigen3/Eigen/ WITH_OPENBLAS= FORCE_DYNAMIC=1 -j 25</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

118

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<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

119

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC119" class="line" lang="markdown">You may need to symlink Eigen in some older versions</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

120

</td>

<td class="diff-line-num new_line 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">

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ln -s $GUIX_ENVIRONMENT/include/eigen3/Eigen src/Eigen</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

122

</td>

<td class="diff-line-num new_line 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">

</td>

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

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

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

</td>

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

<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ~/.config/guix/current/bin/guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl lapack atlas zlib bash ld-wrapper perl ldc</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

114

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

<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make clean ; make WITH_OPENBLAS= FORCE_DYNAMIC=1 -j 25</span></span>

</pre>

</td>

</tr>

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

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

123

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

115

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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

116

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

<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Run tests</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<td class="diff-line-num 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">

117

</td>

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

<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"></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="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,3 +122,31 @@ GEMMA includes the shunit2 test framework (version 2.0).</td>

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

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ./run_tests.sh</span></span>

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

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Releases</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Docker release</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown">To distribute GEMMA I made static versions of the binary. A container</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown">can be made instead with, for example</span>

</pre>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">env </span><span class="nv" style="color: #008080;">GUIX_PACKAGE_PATH</span><span class="o" style="font-weight: 600;">=</span>~/guix-bioinformatics ~/.config/guix/current/bin/guix <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown">  pack <span class="nt" style="color: #000080;">-f</span> docker gemma-gn2 <span class="nt" style="color: #000080;">-S</span> /bin<span class="o" style="font-weight: 600;">=</span>bin</span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown">which created a container in of size 51MB. Tiny! For more information</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown">see</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">GUIX-NOTES</span><span class="p">](</span><span class="sx" style="color: #d14;">http://git.genenetwork.org/guix-bioinformatics/guix-notes/CONTAINERS.org</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Static release</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown">To create a static release, locate the gfortran lib and use</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;">    source .guix-dev-static</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"><span class="sb" style="color: #d14;">    make WITH_GFORTRAN=1 EXTRA_FLAGS=-L/gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib static</span></span>

</pre>

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

</pre>

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown">otherwise OpenBlas will complain with</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;">    undefined reference to `_gfortran_concat_string'</span></span></pre>

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<br>

</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -23,6 +23,10 @@</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#      make static</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#    Static build may require some extra flags</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#      make WITH_GFORTRAN=1 EXTRA_FLAGS=-L/gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib static</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="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="make"><span class="c" style="color: #998; font-style: italic;">#    Run tests with</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#      make check</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,6 +76,7 @@ WITH_GFORTRAN          =                  # Add -lgfortran (if OpenBlas does not</td>

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="make"><span class="nv" style="color: #008080;">OPENBLAS_LEGACY</span>        <span class="o" style="font-weight: 600;">=</span>                  <span class="c" style="color: #998; font-style: italic;"># Using older OpenBlas</span></span>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="make"><span class="nv" style="color: #008080;">FORCE_STATIC</span>           <span class="o" style="font-weight: 600;">=</span>                  <span class="c" style="color: #998; font-style: italic;"># Static linking of libraries</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="make"><span class="nv" style="color: #008080;">GCC_FLAGS</span>              <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DHAVE_INLINE</span> <span class="nt" style="color: #000080;">-pthread</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu++11 <span class="c" style="color: #998; font-style: italic;"># extra flags -Wl,--allow-multiple-definition</span></span>

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<td class="diff-line-num new old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="make"><span class="nv" style="color: #008080;">EXTRA_FLAGS</span>            <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

80

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"><span class="nv" style="color: #008080;">GSL_INCLUDE_PATH</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(SYS), WIN)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -172,6 +177,9 @@ endif</td>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="make"><span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">WITH_GFORTRAN</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="make">  <span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-lgfortran</span> <span class="nt" style="color: #000080;">-lquadmath</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="make"><span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="make">  <span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">$(EXTRA_FLAGS)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all test</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="make"></span>

</pre>

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<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,28 +3,32 @@ Nat. Genet., 2016)](cfw.gif)</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;"># GEMMA: Genome-wide Efficient Mixed Model Association</span></span>

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/genetics-statistics/GEMMA.svg?branch=master</span><span class="p">)</span>](https://travis-ci.<span class="idiff left">org/genetics-statistics/GEMMA) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![Anaconda-Server Badge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/gemma/badges/installer/conda.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://anaconda.org/bioconda/gemma) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![DL</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/gemma/badges/downloads.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://anaconda.org/bioconda/gemma) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![BrewBadge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/badge/%F0%9F%8D%BAbrew-gemma--0.98-brightgreen.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://github.com/brewsci/homebrew-bio) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![GuixBadge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/badge/gnuguix-gemma-brightgreen.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://www.gnu.org/software/guix/packages/G/) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![DebianBadge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://badges.debian.net/badges/debian/testing/gemma/version.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://packages.debian.org/testing/gemma</span>)</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/genetics-statistics/GEMMA.svg?branch=master</span><span class="p">)</span>](https://travis-ci.<span class="idiff left">com/genetics-statistics/GEMMA) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![Anaconda-Server Badge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/gemma/badges/installer/conda.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://anaconda.org/bioconda/gemma) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![DL</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/gemma/badges/downloads.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://anaconda.org/bioconda/gemma) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![BrewBadge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/badge/%F0%9F%8D%BAbrew-gemma--0.98-brightgreen.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://github.com/brewsci/homebrew-bio) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![GuixBadge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://img.shields.io/badge/gnuguix-gemma-brightgreen.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff">](https://www.gnu.org/software/guix/packages/G/) </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">![DebianBadge</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://badges.debian.net/badges/debian/testing/gemma/version.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://packages.debian.org/search?keywords=gemma&searchon=names&suite=all&section=all</span>)</span>

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown">GEMMA is a software toolkit for fast application of linear mixed</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">models (LMMs) and related models to genome-wide association studies</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">(GWAS) and other large-scale data sets.</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">Check out <span class="p">[</span><span class="nv" style="color: #008080;">NEWS.md</span><span class="p">](</span><span class="sx" style="color: #d14;">NEWS.md</span><span class="p">)</span> to see what's new in each GEMMA release.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">Check out <span class="p">[</span><span class="nv" style="color: #008080;">RELEASE-NOTES.md</span><span class="p">](</span><span class="sx" style="color: #d14;">RELEASE-NOTES.md</span><span class="p">)</span> to see what's new in</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">each GEMMA release.</span>

</pre>

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

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">Please post <span class="idiff left right">feature requests or </span>suspected bugs to</span>

</pre>

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

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

15

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<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="markdown">Please post suspected bugs to</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Github issues</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/genetics-statistics/GEMMA/issues</span><span class="p">)</span>. For</span>

</pre>

</td>

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

16

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

17

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown">questions or other discussion, please post to the</span>

</pre>

</td>

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

17

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="p">[</span><span class="nv" style="color: #008080;">GEMMA Google Group</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/group/gemma-discussion</span><span class="p">)</span>. We</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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

<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">also encourage contributions, for example, by forking the repository,</span>

</pre>

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<td class="diff-line-num 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">

19

</td>

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

20

</td>

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">making your changes to the code, and issuing a pull request.</span>

</pre>

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

20

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

21

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

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

</pre>

</td>

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

21

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

</td>

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

<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">Currently, GEMMA is supported for 64-bit Mac OS X and Linux</span>

</pre>

</td>

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

22

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

</td>

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

<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">platforms. <span class="ge" style="font-style: italic;">*Windows is not currently supported.*</span> though you can</span>

</pre>

</td>

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

23

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown">run GEMMA in a Linux VM or <span class="p">[</span><span class="nv" style="color: #008080;">container</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.docker.com/docker-for-windows/</span><span class="p">)</span>. If you are interested</span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">in helping to make GEMMA available on Windows platforms (e.g., by</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">providing installation instructions for Windows, or by contributing</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">Windows binaries) please post a note in the</span>

</pre>

</td>

</tr>

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

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

27

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

</td>

<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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Github issues</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/genetics-statistics/GEMMA/issues</span><span class="p">)</span>.</span>

</pre>

</td>

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

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

22

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<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="markdown">Currently, GEMMA provides a runnable Docker container for 64-bit</span>

</pre>

</td>

</tr>

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

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

23

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<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">MacOS, Windows and Linux platforms. GEMMA can be installed with</span>

</pre>

</td>

</tr>

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

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

24

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<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">Debian, Conda, Homebrew and GNU Guix. With Guix you find the latest</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

25

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<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="markdown">version</span>

</pre>

</td>

</tr>

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

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

26

</td>

<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="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="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="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="markdown">as it is the version we use every day on http://genenetwork.org. For</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">installation instructions see also <span class="p">[</span><span class="nv" style="color: #008080;">INSTALL.md</span><span class="p">](</span><span class="sx" style="color: #d14;">INSTALL.md</span><span class="p">)</span>.  We use</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">continous integration builds on Travis-CI for Linux (amd64 & arm64)</span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">and MacOS (amd64). GEMMA builds on multiple architectures, see the</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Debian build farm</span><span class="p">](</span><span class="sx" style="color: #d14;">https://buildd.debian.org/status/package.php?p=gemma</span><span class="p">)</span>.</span>

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

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>(The above image depicts physiological and behavioral trait</span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown">loci identified in CFW mice using GEMMA, from <span class="p">[</span><span class="nv" style="color: #008080;">Parker et al, Nature</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">@@ -50,19 +54,19 @@ Genetics, 2016](https://doi.org/10.1038/ng.3609).)</td>

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

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="p">1.</span> Fast assocation tests implemented using the univariate linear mixed</span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown">model (LMM). In GWAS, this can correct for population structure and</span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown">sample nonexchangeability. It also provides estimates of the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">sample non<span class="idiff left right">-</span>exchangeability. It also provides estimates of the</span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown">proportion of variance in phenotypes explained by available genotypes</span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">(PVE), often called "chip heritability" or "SNP heritability".</span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="p">2.</span> Fast association tests for multiple phenotypes implemented using a</span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown">multivariate linear mixed model (mvLMM). In GWAS, this can correct for</span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">population<span class="idiff left right">s tructure and sample nonexchangeability jointly in multiple</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">complex phenotypes.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">population<span class="idiff left right"> structure and sample (non)exchangeability - jointly in</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="idiff left right">multiple </span>complex phenotypes.</span>

</pre>

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="p">3.</span> Bayesian sparse linear mixed model (BSLMM) for estimating PVE,</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown">phenotype prediction, and multi-marker modeling in GWAS.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="p">4.</span> Estimation of variance components ("chip heritability") partitioned</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">4.</span> Estimation of variance components ("chip<span class="idiff left right">/SNP</span> heritability") partitioned</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown">by different SNP functional categories from raw (individual-level)</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown">data or summary data. For raw data, HE regression or the REML AI</span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">algorithm can be used to estimate variance components when</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +77,8 @@ MQS algorithm to estimate variance components.</td>

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

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown">To install GEMMA you can</span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown"><span class="p">1.</span> Download the precompiled binaries (64-bit Linux and Mac only)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">1.</span> Download the precompiled or Docker binaries</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">   from <span class="p">[</span><span class="nv" style="color: #008080;">releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/genetics-statistics/GEMMA/releases</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="p">2.</span> Use existing package managers, see <span class="p">[</span><span class="nv" style="color: #008080;">INSTALL.md</span><span class="p">](</span><span class="sx" style="color: #d14;">INSTALL.md</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); 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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,20 +93,16 @@ numerical libraries.</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="p">1.</span> Fetch the <span class="p">[</span><span class="nv" style="color: #008080;">latest stable release</span><span class="p">][</span><span class="ss" style="color: #990073;">latest_release</span><span class="p">]</span> and download the</span>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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

<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">   file appropriate for your platform.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

</td>

<td class="diff-line-num new_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">

95

</td>

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

<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

</td>

<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC91" class="line" lang="markdown"><span class="p">2.</span> For .tar.bz2 files unpack the tar ball</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="p">2.</span> For Docker images, install Docker, load the image into Docker and</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

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

<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown">   run with something like</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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

98

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

<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

93

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC93" class="line" lang="markdown"><span class="sb" style="color: #d14;">        tar xvjf gemma-$version-installer.tar.bz2</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

94

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC94" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

95

</td>

<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;">    run the installer</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

96

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC96" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

97

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC97" class="line" lang="markdown"><span class="sb" style="color: #d14;">        ./install.sh ~/gemma</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

98

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC98" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

99

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC99" class="line" lang="markdown"><span class="sb" style="color: #d14;">    and run gemma</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

100

</td>

<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC100" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

101

</td>

<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(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="LC101" class="line" lang="markdown"><span class="sb" style="color: #d14;">        ~/gemma/bin/gemma</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

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

<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="sb" style="color: #d14;">        docker run -w /run -v ${PWD}:/run ed5bf7499691 gemma -gk -bfile example/mouse_hs1940</span></span>

</pre>

</td>

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

102

</td>

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

100

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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

101

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

<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="p">3.</span> For .gz files run <span class="sb" style="color: #d14;">`gunzip gemma.linux.gz`</span> or <span class="sb" style="color: #d14;">`gunzip</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

104

</td>

<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(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="LC104" class="line" lang="markdown"><span class="sb" style="color: #d14;">gemma.linux.gz`</span> to unpack the file.</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

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

<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="sb" style="color: #d14;">gemma.linux.gz`</span> to unpack the file. And make sure it is executable with</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="sb" style="color: #d14;">        chmod u+x gemma-linux</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="sb" style="color: #d14;">        ./gemma-linux</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Run GEMMA</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,24 +132,25 @@ Above example files can be downloaded from</td>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown">GEMMA has a wide range of debugging options which can be viewed with</span>

</pre>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC134" class="line" lang="markdown">gemma -h 14</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC135" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"> DEBUG OPTIONS</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown"> -check                   enable checks (slower)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"> -no-fpe-check            disable hardware floating point checking</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"> -strict                  strict mode will stop when there is a problem</span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"> -silence                 silent terminal display</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"> -debug                   debug output</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"> -debug-data              debug data output</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"> -nind       [num]        read up to num individuals</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"> -issue      [num]        enable tests relevant to issue tracker</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"> -legacy                  run gemma in legacy mode</span>

</pre>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC146" class="line" lang="markdown">typically when running gemma you should use -debug which includes relevant</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC147" class="line" lang="markdown">checks.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC148" class="line" lang="markdown">typically when running gemma you should use -debug which includes</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown">relevant checks. When compiled for debugging the debug version of</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown">GEMMA gives more information.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="markdown">For performances you may want to use the -no-check option</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown">instead. Also check the build optimization notes in</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">INSTALL.md</span><span class="p">](</span><span class="sx" style="color: #d14;">INSTALL.md</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown">For performance you may want to use the -no-check option. Also check</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown">the build optimization notes in <span class="p">[</span><span class="nv" style="color: #008080;">INSTALL.md</span><span class="p">](</span><span class="sx" style="color: #d14;">INSTALL.md</span><span class="p">)</span>.</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Help</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,7 +193,7 @@ studies.](https://doi.org/10.1101/042846) *Annals of Applied Statistics*, in pre</td>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

</td>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC194" class="line" lang="markdown">Copyright (C) 2012–20<span class="idiff left right">18</span>, Xiang Zhou and team.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown">Copyright (C) 2012–20<span class="idiff left right">20</span>, Xiang Zhou and team.</span>

</pre>

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195

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197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

196

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<td class="diff-line-num new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="markdown">The <span class="ge" style="font-style: italic;">*GEMMA*</span> source code repository is free software: you can</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown">redistribute it under the terms of the</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#6f8a88f369eae9b2f3ece90d1ba6366a16f25f9c"><strong>RELEASE-NOTES.md</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="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">@@ -4,6 +4,15 @@ see</td>

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

4

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

4

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">commits</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/genetics-statistics/GEMMA/commits/master</span><span class="p">)</span>.</span>

</pre>

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

6

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<td class="diff-line-num new_line" data-linenumber="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="markdown"></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.98.4 (2021/01/29)</span></span>

</pre>

</td>

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

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

8

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

</pre>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> Fix error on free with randomizer, see #239</span>

</pre>

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

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

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> Moved travis-ci.org to travis-ci.com</span>

</pre>

</td>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> GEMMA builds on ARM and other architectures, see #189 and https://buildd.debian.org/status/package.php?p=gemma (thanks @tillea)</span>

</pre>

</td>

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

</td>

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

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">*</span> Fixed static build with 00480e8549987b6cae7100b28bcead2a2d501177 - requires gfortran path for OpenBLAS</span>

</pre>

</td>

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

</td>

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

13

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">*</span> Updated README's and Manual</span>

</pre>

</td>

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

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

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">*</span> Added <span class="sb" style="color: #d14;">`-lmm 9`</span> switch which shows ~beta/se~ with ~lmle~ and ~plrt~, see #237</span>

</pre>

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

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

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

</pre>

</td>

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

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.98.3 (2020/11/28)</span></span>

</pre>

</td>

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

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +30,15 @@ Maintenance release</td>

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

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">  <span class="p">[</span><span class="nv" style="color: #008080;">docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.gnu.org/software/gsl/doc/html/rng.html</span><span class="p">)</span>.</span>

</pre>

</td>

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

22

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="p">*</span> The tests now use a fixed seed for the randomizer</span>

</pre>

</td>

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

23

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

32

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

</pre>

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

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

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">A docker binary that runs on Linux, MaxOS and Windows can be downloaded from</span>

</pre>

</td>

</tr>

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

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34

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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="LC34" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">http://ipfs.genenetwork.org/ipfs/Qmaq1q73ox53ykKdRF6tYDXL9bEKJQfnGCqBxFdo1fcYPb/gemma-0.98.3-AMD64-Guix-docker-release.tgz</span>

</pre>

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

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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="markdown">After loading the image into Docker, run with something like</span>

</pre>

</td>

</tr>

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

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

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

<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"></span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="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="markdown"><span class="sb" style="color: #d14;">    docker run -w /run -v ${PWD}:/run ed5bf7499691 gemma -gk -bfile example/mouse_hs1940</span></span>

</pre>

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>

</pre>

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

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

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

</pre>

</td>

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

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<td class="diff-line-num new_line" data-linenumber="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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## ChangeLog v0.98.2 (2019/05/28)</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="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="markdown"></span>

</pre>

</td>

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

26

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

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown">GCC 10.1 fix release</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>

<hr>

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

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1

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0.98.<span class="idiff left right">3</span></span></pre>

</td>

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

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0.98.<span class="idiff left right">4</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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

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

</td>

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

1

</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gemma (0.98.4+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

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

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

2

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

</pre>

</td>

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

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

3

</td>

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

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

</pre>

</td>

</tr>

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4

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

</pre>

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5

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

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com>  Wed, 03 Feb 2021 01:29:26 +0530</span>

</pre>

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7

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

</pre>

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1

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

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">gemma (0.98.3+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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

9

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

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3

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

10

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

</pre>

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<br>

</li>

<li id="f6361e25b2927c77444e8b661a216d7f56f9d1f8">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#f6361e25b2927c77444e8b661a216d7f56f9d1f8"><strong>debian/patches/Makefile.patch</strong></a>

<hr>

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<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 @@ Last-Update: 2018-04-26</td>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/Makefile</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>

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

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">19,7 +219,7 @@</span></span><span class="idiff right"> $(OBJS): $(HDR)</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">25,7 +225,7 @@</span></span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> .SUFFIXES : .cpp .c .o $(SUFFIXES)</span>

</pre>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ Last-Update: 2018-04-26</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff">  $(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o  $(TEST_SRC_DIR)/unittests-math.o $(filter-out src/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> unittests: all ./bin/unittests-gemma</span>

</pre>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">28,12 +228,12 @@</span></span><span class="idiff right"> unittests: all ./bin/unittests-gemma</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">34,12 +234,12 @@</span></span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> fast-check: all unittests</span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff">  rm -vf test/output/*</span>

</pre>

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff">  cd test && ./dev_test_suite.sh | tee ../dev_test.log</span>

</pre>

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<br>

</li>

<li id="26b6c1e1d4b838bcdd860d7c24ef8ef3b521d33f">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#26b6c1e1d4b838bcdd860d7c24ef8ef3b521d33f"><strong>debian/patches/Reproducible_builds.patch</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,11 +3,9 @@ Description: Patch the makefile in order to enable reproducible builds (stable o</td>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2018-06-14</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Forwarded: TODO</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Index: gemma-0.98+dfsg/Makefile</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gemma-0.98+dfsg.orig/Makefile</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ gemma-0.98+dfsg/Makefile</span></span>

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -215,8 +215,8 @@</span> ifdef WITH_LAPACK</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/Makefile</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -201,8 +201,8 @@</span></span>

</pre>

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

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>

</pre>

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<br>

</li>

<li id="4adf3f896c0b9b2ec23e956edfbf787c4ffec48c">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#4adf3f896c0b9b2ec23e956edfbf787c4ffec48c"><strong>debian/patches/no-lquadmath.patch</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,12 +6,12 @@ Bug-Debian: https://bugs.debian.org/902153</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- a/Makefile</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -17<span class="idiff left">2,7 +172,7 @@</span></span><span class="idiff right"> ifdef WITH_GSLCBLAS</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -17<span class="idiff left right">5,7 +175,7 @@</span></span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff">   LIBS += -lgslcblas</span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> endif</span>

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  LIBS += -lgfortran -lquadmath</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  LIBS += -lgfortran</span></span>

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

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> <span class="idiff left right">.PHONY: all test</span></span></pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> <span class="idiff left right">ifdef EXTRA_FLAGS</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> <span class="idiff left right">  LIBS += $(EXTRA_FLAGS)</span></span></pre>

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<br>

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<li id="8799e0764d072adeaa173a1402f03a70ad62b5bd">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#8799e0764d072adeaa173a1402f03a70ad62b5bd"><strong>doc/manual.pdf</strong></a>

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<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#708cbc7b584b2f8ebbf34725c60b059470cd4c33"><strong>doc/manual.tex</strong></a>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,7 @@ association studies (GWAS). It fits a univariate linear mixed model</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="tex">(LMM) for marker association tests with a single phenotype to account</span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="tex">for population stratification and sample structure, and for estimating</span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="tex">the proportion of variance in phenotypes explained (PVE) by typed</span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="tex">genotypes (i.e. <span class="idiff left right">"chip heritability"</span>) <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>Zhou:2012<span class="p">}</span>. It fits a</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="tex">genotypes (i.e. <span class="idiff left right">``chip heritability'' or ``SNP heritability''</span>) <span class="k" style="font-weight: 600;">\cite</span><span class="p">{</span>Zhou:2012<span class="p">}</span>. It fits a</span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="tex">multivariate linear mixed model (mvLMM) for testing marker</span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="tex">associations with multiple phenotypes simultaneously while controlling</span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="tex">for population stratification, and for estimating genetic correlations</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">@@ -124,7 +124,8 @@ labels) for $n$ individuals; $\bW=(\bw_1, \cdots, \bw_c)$ is an</td>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="tex"><span class="p">$</span><span class="nb" style="color: #0086b3;">n</span><span class="nv" style="color: #008080;">\times</span><span class="nb" style="color: #0086b3;"> c</span><span class="p">$</span> matrix of covariates (fixed effects) including a column of</span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="tex">1s; <span class="p">$</span><span class="nv" style="color: #008080;">\boldsymbol</span><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">\alpha</span><span class="p">$</span> is a <span class="p">$</span><span class="nb" style="color: #0086b3;">c</span><span class="p">$</span>-vector of the corresponding</span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="tex">coefficients including the intercept; <span class="p">$</span><span class="nv" style="color: #008080;">\bx</span><span class="p">$</span> is an <span class="p">$</span><span class="nb" style="color: #0086b3;">n</span><span class="p">$</span>-vector of marker</span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="tex">genotypes; <span class="p">$</span><span class="nv" style="color: #008080;">\beta</span><span class="p">$</span> is the effect size of the marker; <span class="p">$</span><span class="nv" style="color: #008080;">\bu</span><span class="p">$</span> is an</span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="tex">genotypes; <span class="p">$</span><span class="nv" style="color: #008080;">\beta</span><span class="p">$</span> is the effect size of the marker and is an estimate</span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="tex"> of the marker/SNP additive effect; <span class="p">$</span><span class="nv" style="color: #008080;">\bu</span><span class="p">$</span> is an</span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="tex"><span class="p">$</span><span class="nb" style="color: #0086b3;">n</span><span class="p">$</span>-vector of random effects; <span class="p">$</span><span class="nv" style="color: #008080;">\bepsilon</span><span class="p">$</span> is an <span class="p">$</span><span class="nb" style="color: #0086b3;">n</span><span class="p">$</span>-vector of errors;</span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="tex"><span class="p">$</span><span class="nv" style="color: #008080;">\tau</span><span class="p">^{</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">}$</span> is the variance of the residual errors; <span class="p">$</span><span class="nv" style="color: #008080;">\lambda</span><span class="p">$</span> is the</span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="tex">ratio between the two variance components; <span class="p">$</span><span class="nv" style="color: #008080;">\bK</span><span class="p">$</span> is a known <span class="p">$</span><span class="nb" style="color: #0086b3;">n</span><span class="nv" style="color: #008080;">\times</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">@@ -139,8 +140,8 @@ score). GEMMA obtains either the maximum likelihood estimate (MLE) or</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="tex">the restricted maximum likelihood estimate (REML) of <span class="p">$</span><span class="nv" style="color: #008080;">\lambda</span><span class="p">$</span> and</span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="tex"><span class="p">$</span><span class="nv" style="color: #008080;">\beta</span><span class="p">$</span>, and outputs the corresponding <span class="p">$</span><span class="nb" style="color: #0086b3;">p</span><span class="p">$</span> value.</span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="tex"></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="tex">In addition, GEMMA estimates the PVE by typed genotypes or ``chip</span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="tex"><span class="idiff left right">heritability"</span>.</span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="tex">In addition, GEMMA estimates the PVE by typed genotypes or ``chip<span class="idiff left right"> or</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="tex"><span class="idiff left right">SNP heritability''</span>.</span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="tex"><span class="k" style="font-weight: 600;">\subsubsection</span><span class="p">{</span>Multivariate Linear Mixed Model<span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="tex">GEMMA can fit a multivariate linear mixed model in the following form:</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">@@ -307,19 +308,12 @@ platform.</td>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="tex">The binary executable of GEMMA works well for a reasonably large</span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="tex">number of individuals (say, for example, the ``-eigen " option works</span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="tex">for at least 45,000 individuals). Due to the outdated computation</span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="tex">environment the software was compiled on, however, for larger sample</span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="tex">size and for improved computation efficiency, it is recommended to</span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="tex">compile GEMMA on user's own modern computer system.</span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="tex">for at least 45,000 individuals).</span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="tex">If you want to compile GEMMA by yourself, you will need to download</span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="tex">the source code, and you will need a standard C/C++ compiler such as</span>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="tex">GNU gcc, as well as the GSL and LAPACK libraries. You will need to</span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="tex">change the library paths in the Makefile accordingly. A sample</span>

</pre>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="tex">Makefile is provided along with the source code. For details on</span>

</pre>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="tex">installing GSL library, please refer to</span>

</pre>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="tex"><span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>http://www.gnu.org/s/gsl/<span class="p">}</span>. For details on installing LAPACK</span>

</pre>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="tex">library, please refer to <span class="k" style="font-weight: 600;">\url</span><span class="p">{</span>http://www.netlib.org/lapack/<span class="p">}</span>.</span>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="tex">GNU gcc, as well as GSL and OpenBLAS libraries.  A sample</span>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="tex">Makefile is provided along with the source code.</span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="tex"></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="tex"><span class="k" style="font-weight: 600;">\newpage</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="tex"></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">@@ -334,7 +328,7 @@ genotypes and using BIMBAM files for phenotypes) will result in</td>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="tex">unwanted errors. BIMBAM format is particularly useful for imputed</span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="tex">genotypes, as PLINK codes genotypes using 0/1/2, while BIMBAM can</span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="tex">accommodate any real values between 0 and 2 (and any real values if</span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="tex">paired with ``-notsnp<span class="idiff left right">"</span> option). In addition, to estimate variance</span>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="tex">paired with ``-notsnp<span class="idiff left right">''</span> option). In addition, to estimate variance</span>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="tex">components using summary statistics, GEMMA requires two other input</span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="tex">files: one contains marginal z-scores and the other contains SNP</span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="tex">category.</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); 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="803" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -809,7 +803,11 @@ chr     rs      ps      n_mis   n_obs   allele1 allele0 af      beta    se</td>

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<pre style="margin: 0;"> <span id="LC803" class="line" lang="tex"><span class="nv" style="color: #008080;">\end</span><span class="p">{</span><span class="nb" style="color: #0086b3;">verbatim</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC804" class="line" lang="tex"><span class="c" style="color: #998; font-style: italic;">%</span></span>

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<pre style="margin: 0;"> <span id="LC805" class="line" lang="tex"></span>

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<td class="diff-line-num new_line old" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC812" class="line" lang="tex"><span class="nb" style="color: #0086b3;">The </span><span class="m" style="color: #099;">11</span><span class="nb" style="color: #0086b3;"> columns are: chromosome numbers, snp ids, base pair positions on the chromosome, number of missing individuals for a given snp, number of non</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">missing individuals for a given snp, minor allele, major allele, allele frequency, beta estimates, standard errors for beta, and </span><span class="p">$</span>p<span class="p">$</span><span class="nb" style="color: #0086b3;"> values from the Wald test.</span></span>

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="tex"><span class="nb" style="color: #0086b3;">The </span><span class="m" style="color: #099;">11</span><span class="nb" style="color: #0086b3;"> columns are: chromosome numbers, snp ids, base pair positions</span></span>

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<td class="diff-line-num new new_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="tex"><span class="nb" style="color: #0086b3;">on the chromosome, number of missing individuals for a given snp,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

808

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<pre style="margin: 0;">+<span id="LC808" class="line" lang="tex"><span class="nb" style="color: #0086b3;">number of non</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">missing individuals for a given snp, minor allele, major</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

809

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<pre style="margin: 0;">+<span id="LC809" class="line" lang="tex"><span class="nb" style="color: #0086b3;">allele, allele frequency, beta estimates </span><span class="o" style="font-weight: 600;">(</span><span class="nb" style="color: #0086b3;">additive effect</span><span class="o" style="font-weight: 600;">)</span><span class="nb" style="color: #0086b3;">, standard</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

810

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="tex"><span class="nb" style="color: #0086b3;">errors for beta, and </span><span class="p">$</span>p<span class="p">$</span><span class="nb" style="color: #0086b3;"> values from the Wald test.</span></span>

</pre>

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813

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<td class="diff-line-num new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="tex"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

814

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<td class="diff-line-num new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

812

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<pre style="margin: 0;"> <span id="LC812" class="line" lang="tex"><span class="nv" style="color: #008080;">\subsection</span><span class="p">{</span><span class="nb" style="color: #0086b3;">Estimate Relatedness Matrix from Genotypes</span><span class="p">}</span></span>

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815

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813

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<pre style="margin: 0;"> <span id="LC813" class="line" lang="tex"></span>

</pre>

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<br>

</li>

<li id="8830c9ed5fb31e949b61cb9b0e6e4a49f2d44d55">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#8830c9ed5fb31e949b61cb9b0e6e4a49f2d44d55"><strong>guix.scm</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;; To use this file to build HEAD of gemma:</span></span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;;</span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;;   guix build -f guix.scm</span></span>

</pre>

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;;</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;; To get a development container (e.g., run in emacs shell).</span></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;;</span></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="scheme"><span class="c1" style="color: #998; font-style: italic;">;;   guix environment -C -l guix.scm</span></span>

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8

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

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="scheme"><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">use-modules</span></span>

</pre>

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

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="scheme">  <span class="p">((</span><span class="nf" style="color: #900; font-weight: 600;">guix</span> <span class="nv" style="color: #008080;">licenses</span><span class="p">)</span> <span class="o" style="font-weight: 600;">#</span><span class="nv" style="color: #008080;">:prefix</span> <span class="nv" style="color: #008080;">license:</span><span class="p">)</span></span>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">guix</span> <span class="nv" style="color: #008080;">gexp</span><span class="p">)</span></span>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">guix</span> <span class="nv" style="color: #008080;">packages</span><span class="p">)</span></span>

</pre>

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

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">guix</span> <span class="nv" style="color: #008080;">git-download</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">guix</span> <span class="nv" style="color: #008080;">build-system</span> <span class="nv" style="color: #008080;">meson</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

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

15

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<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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">algebra</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">base</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

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

17

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<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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">compression</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

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

18

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<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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">bioinformatics</span><span class="p">)</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">build-tools</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

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

20

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

<pre style="margin: 0;">+<span id="LC20" class="line" lang="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">curl</span><span class="p">)</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">llvm</span><span class="p">)</span></span>

</pre>

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

</td>

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

22

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<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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">maths</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">ninja</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">parallel</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">perl</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">perl6</span><span class="p">)</span></span>

</pre>

</td>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">gnu</span> <span class="nv" style="color: #008080;">packages</span> <span class="nv" style="color: #008080;">pkg-config</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="scheme">  <span class="c1" style="color: #998; font-style: italic;">;; (gnu packages shell)  ;; for shunit2</span></span>

</pre>

</td>

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

</td>

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

29

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<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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">srfi</span> <span class="nv" style="color: #008080;">srfi-1</span><span class="p">)</span></span>

</pre>

</td>

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

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

</td>

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

30

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<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="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">ice-9</span> <span class="nv" style="color: #008080;">popen</span><span class="p">)</span></span>

</pre>

</td>

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

31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">ice-9</span> <span class="nv" style="color: #008080;">rdelim</span><span class="p">))</span></span>

</pre>

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

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

32

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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="LC32" class="line" lang="scheme"></span>

</pre>

</td>

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

</td>

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

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="scheme"><span class="p">(</span><span class="k" style="font-weight: 600;">define</span> <span class="nv" style="color: #008080;">%source-dir</span> <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span> <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">current-filename</span><span class="p">)))</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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

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

</pre>

</td>

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

</td>

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

35

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="scheme"><span class="p">(</span><span class="k" style="font-weight: 600;">define</span> <span class="nv" style="color: #008080;">%git-commit</span></span>

</pre>

</td>

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

</td>

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

36

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">read-string</span> <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">open-pipe</span> <span class="s" style="color: #d14;">"git show HEAD | head -1 | cut -d ' ' -f 2"</span> <span class="nv" style="color: #008080;">OPEN_READ</span><span class="p">)))</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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

<pre style="margin: 0;">+<span id="LC37" class="line" lang="scheme"></span>

</pre>

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

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

38

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

<pre style="margin: 0;">+<span id="LC38" class="line" lang="scheme"><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">define-public</span> <span class="nv" style="color: #008080;">gemma-git</span></span>

</pre>

</td>

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

</td>

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

39

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

<pre style="margin: 0;">+<span id="LC39" class="line" lang="scheme">  <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">package</span></span>

</pre>

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC40" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">name</span> <span class="s" style="color: #d14;">"gemma-git"</span><span class="p">)</span></span>

</pre>

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

</td>

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

41

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

<pre style="margin: 0;">+<span id="LC41" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">version</span> <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">git-version</span> <span class="s" style="color: #d14;">"0.98.4"</span> <span class="s" style="color: #d14;">"HEAD"</span> <span class="nv" style="color: #008080;">%git-commit</span><span class="p">))</span></span>

</pre>

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

</td>

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

42

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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="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">source</span> <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">local-file</span> <span class="nv" style="color: #008080;">%source-dir</span> <span class="o" style="font-weight: 600;">#</span><span class="nv" style="color: #008080;">:recursive?</span> <span class="no" style="color: #008080;">#t</span><span class="p">))</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">build-system</span> <span class="nv" style="color: #008080;">meson-build-system</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

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

44

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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="LC44" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">inputs</span> <span class="o" style="font-weight: 600;">`</span><span class="p">(</span></span>

</pre>

</td>

</tr>

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

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

</td>

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

45

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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="LC45" class="line" lang="scheme">              <span class="p">(</span><span class="s" style="color: #d14;">"gsl"</span> <span class="o" style="font-weight: 600;">,</span><span class="nv" style="color: #008080;">gsl</span><span class="p">)</span></span>

</pre>

</td>

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

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

</td>

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

46

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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="scheme">              <span class="c1" style="color: #998; font-style: italic;">;; ("shunit2" ,shunit2) ;; comes with gemma</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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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="LC47" class="line" lang="scheme">              <span class="p">(</span><span class="s" style="color: #d14;">"openblas"</span> <span class="o" style="font-weight: 600;">,</span><span class="nv" style="color: #008080;">openblas</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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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="LC48" class="line" lang="scheme">              <span class="p">(</span><span class="s" style="color: #d14;">"zlib"</span> <span class="o" style="font-weight: 600;">,</span><span class="nv" style="color: #008080;">zlib</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

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

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

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">native-inputs</span> <span class="c1" style="color: #998; font-style: italic;">; for running tests</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="scheme">     <span class="o" style="font-weight: 600;">`</span><span class="p">((</span><span class="s" style="color: #d14;">"perl"</span> <span class="o" style="font-weight: 600;">,</span><span class="nv" style="color: #008080;">perl</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="scheme">       <span class="p">(</span><span class="s" style="color: #d14;">"which"</span> <span class="o" style="font-weight: 600;">,</span><span class="nv" style="color: #008080;">which</span><span class="p">)</span></span>

</pre>

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

53

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="scheme">       <span class="p">))</span></span>

</pre>

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

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

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">home-page</span> <span class="s" style="color: #d14;">"https://github.com/genetics-statistics"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">synopsis</span> <span class="s" style="color: #d14;">"Tool for genome-wide efficient mixed model association"</span><span class="p">)</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">description</span> <span class="s" style="color: #d14;">"Genome-wide Efficient Mixed Model Association (GEMMA)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="scheme"><span class="s" style="color: #d14;">provides a standard linear mixed model resolver with application in</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="scheme"><span class="s" style="color: #d14;">genome-wide association studies (GWAS)."</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="scheme">    <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">license</span> <span class="nv" style="color: #008080;">license:gpl3</span><span class="p">)))</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="scheme"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="scheme"><span class="nv" style="color: #008080;">gemma-git</span></span></pre>

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<br>

</li>

<li id="7e010836fc66dfe28d372f4533ed86ba8aa18834">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#7e010836fc66dfe28d372f4533ed86ba8aa18834"><strong>src/gemma.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2550" style="width: 35px; color: rgba(0,0,0,0.3); 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="2550" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2550,8 +2550,8 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<pre style="margin: 0;"> <span id="LC2550" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2551" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// LMM or mvLMM or Eigen-Decomposition</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2552" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM3</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2553" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM4</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM5</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2554" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_EIGEN</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Fit LMM or mvLMM or eigen</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2553" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM4</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_LMM5</span> <span class="o" style="font-weight: 600;">||</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">||</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2554" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_EIGEN</span><span class="idiff left right">  </span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Fit LMM or mvLMM or eigen</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2555" class="line" lang="cpp">    <span class="n" style="color: #333;">gsl_matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_matrix_safe_alloc</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">ni_test</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">n_ph</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2556

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<td class="diff-line-num new_line" data-linenumber="2556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2556" class="line" lang="cpp">    <span class="n" style="color: #333;">enforce_msg</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="p">,</span> <span class="s" style="color: #d14;">"allocate Y"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// just to be sure</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2557" class="line" lang="cpp">    <span class="n" style="color: #333;">gsl_matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">W</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_matrix_safe_alloc</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size1</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">n_cvt</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); 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="2565" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2565,6 +2565,7 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2565" class="line" lang="cpp">    <span class="n" style="color: #333;">gsl_vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eval</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_vector_calloc</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2566

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<td class="diff-line-num new_line" data-linenumber="2566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2566" class="line" lang="cpp">    <span class="n" style="color: #333;">gsl_vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">env</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_vector_safe_alloc</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2567

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<td class="diff-line-num new_line" data-linenumber="2567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2567" class="line" lang="cpp">    <span class="n" style="color: #333;">gsl_vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_vector_safe_alloc</span><span class="p">(</span><span class="n" style="color: #333;">Y</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2568" class="line" lang="cpp">    <span class="n" style="color: #333;">debug_msg</span><span class="p">(</span><span class="s" style="color: #d14;">"Started on LMM"</span><span class="p">);</span></span>

</pre>

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2568

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<td class="diff-line-num new_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2569

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<pre style="margin: 0;"> <span id="LC2569" class="line" lang="cpp">    <span class="n" style="color: #333;">assert_issue</span><span class="p">(</span><span class="n" style="color: #333;">is_issue</span><span class="p">(</span><span class="mi" style="color: #099;">26</span><span class="p">),</span> <span class="n" style="color: #333;">UtY</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</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="mf" style="color: #099;">0.0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2569

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<td class="diff-line-num new_line" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2570

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<pre style="margin: 0;"> <span id="LC2570" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2570

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<td class="diff-line-num new_line" data-linenumber="2571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2571

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<pre style="margin: 0;"> <span id="LC2571" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// set covariates matrix W and phenotype matrix Y</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2578" style="width: 35px; color: rgba(0,0,0,0.3); 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="2579" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2578,6 +2579,7 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<pre style="margin: 0;"> <span id="LC2579" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">file_kin</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2579

</td>

<td class="diff-line-num new_line" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2580

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<pre style="margin: 0;"> <span id="LC2580" class="line" lang="cpp">      <span class="n" style="color: #333;">ReadFile_kin</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">file_kin</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">indicator_idv</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">mapID2num</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2580

</td>

<td class="diff-line-num new_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2581

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

<pre style="margin: 0;"> <span id="LC2581" class="line" lang="cpp">                   <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">k_mode</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">,</span> <span class="n" style="color: #333;">G</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2582

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<pre style="margin: 0;">+<span id="LC2582" class="line" lang="cpp">      <span class="n" style="color: #333;">debug_msg</span><span class="p">(</span><span class="s" style="color: #d14;">"Read K/GRM file"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2581

</td>

<td class="diff-line-num new_line" data-linenumber="2583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2583

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<pre style="margin: 0;"> <span id="LC2583" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2582

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<td class="diff-line-num new_line" data-linenumber="2584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2584

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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="cpp">        <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"error! fail to read kinship/relatedness file. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2583

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<td class="diff-line-num new_line" data-linenumber="2585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2585

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<pre style="margin: 0;"> <span id="LC2585" 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="diff-line-num unfold js-unfold old_line" data-linenumber="2609" style="width: 35px; color: rgba(0,0,0,0.3); 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="2611" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2609,7 +2611,7 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="2609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2609

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<td class="diff-line-num new_line" data-linenumber="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2611

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<pre style="margin: 0;"> <span id="LC2611" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2610

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<td class="diff-line-num new_line" data-linenumber="2612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2612

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<pre style="margin: 0;"> <span id="LC2612" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2611

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<td class="diff-line-num new_line" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2613

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<pre style="margin: 0;"> <span id="LC2613" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2612

</td>

<td class="diff-line-num new_line old" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2612" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// eigen-decomposition and calculate trace_G</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2614

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<pre style="margin: 0;">+<span id="LC2614" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// eigen-decomposition and calculate trace_G<span class="idiff left right"> - main track</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2613

</td>

<td class="diff-line-num new_line" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2615

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

<pre style="margin: 0;"> <span id="LC2615" class="line" lang="cpp">      <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Start Eigen-Decomposition..."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2614

</td>

<td class="diff-line-num new_line" data-linenumber="2616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2616

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<pre style="margin: 0;"> <span id="LC2616" class="line" lang="cpp">      <span class="n" style="color: #333;">time_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2615

</td>

<td class="diff-line-num new_line" data-linenumber="2617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2617

</td>

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

<pre style="margin: 0;"> <span id="LC2617" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); 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="2665" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2663,7 +2665,7 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="2663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2663

</td>

<td class="diff-line-num new_line" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2665

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<pre style="margin: 0;"> <span id="LC2665" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">M_EIGEN</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2664

</td>

<td class="diff-line-num new_line" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2666

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<pre style="margin: 0;"> <span id="LC2666" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">WriteMatrix</span><span class="p">(</span><span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="s" style="color: #d14;">"eigenU"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2665

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<td class="diff-line-num new_line" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2667

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<pre style="margin: 0;"> <span id="LC2667" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">WriteVector</span><span class="p">(</span><span class="n" style="color: #333;">eval</span><span class="p">,</span> <span class="s" style="color: #d14;">"eigenD"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2666

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<td class="diff-line-num new_line old" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2666" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">file_gene</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2668

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<pre style="margin: 0;">+<span id="LC2668" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">file_gene</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// Run with gene file</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2667

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<td class="diff-line-num new_line" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2669

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<pre style="margin: 0;"> <span id="LC2669" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// calculate UtW and Uty</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2668

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<td class="diff-line-num new_line" data-linenumber="2670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2670

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<pre style="margin: 0;"> <span id="LC2670" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcUtX</span><span class="p">(</span><span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">W</span><span class="p">,</span> <span class="n" style="color: #333;">UtW</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2669

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<td class="diff-line-num new_line" data-linenumber="2671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2671

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<pre style="margin: 0;"> <span id="LC2671" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcUtX</span><span class="p">(</span><span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">Y</span><span class="p">,</span> <span class="n" style="color: #333;">UtY</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); 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="2684" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2682,6 +2684,7 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2682

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<td class="diff-line-num new_line" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2684

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<pre style="margin: 0;"> <span id="LC2684" class="line" lang="cpp">      <span class="n" style="color: #333;">cLmm</span><span class="p">.</span><span class="n" style="color: #333;">WriteFiles</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2683

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<td class="diff-line-num new_line" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2685

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<pre style="margin: 0;"> <span id="LC2685" class="line" lang="cpp">      <span class="n" style="color: #333;">cLmm</span><span class="p">.</span><span class="n" style="color: #333;">CopyToParam</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2684

</td>

<td class="diff-line-num new_line" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2686

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<pre style="margin: 0;"> <span id="LC2686" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2687

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<pre style="margin: 0;">+<span id="LC2687" class="line" lang="cpp">      <span class="n" style="color: #333;">debug_msg</span><span class="p">(</span><span class="s" style="color: #d14;">"Main LMM track"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2685

</td>

<td class="diff-line-num new_line" data-linenumber="2688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2688

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<pre style="margin: 0;"> <span id="LC2688" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// calculate UtW and Uty</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2686

</td>

<td class="diff-line-num new_line" data-linenumber="2689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2689

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<pre style="margin: 0;"> <span id="LC2689" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcUtX</span><span class="p">(</span><span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">W</span><span class="p">,</span> <span class="n" style="color: #333;">UtW</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2687

</td>

<td class="diff-line-num new_line" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2690

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<pre style="margin: 0;"> <span id="LC2690" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcUtX</span><span class="p">(</span><span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">Y</span><span class="p">,</span> <span class="n" style="color: #333;">UtY</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="2736" style="width: 35px; color: rgba(0,0,0,0.3); 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="2739" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2736,6 +2739,7 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="2736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2736

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<td class="diff-line-num new_line" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2739

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<pre style="margin: 0;"> <span id="LC2739" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2737

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<td class="diff-line-num new_line" data-linenumber="2740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2740

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<pre style="margin: 0;"> <span id="LC2740" class="line" lang="cpp">        <span class="n" style="color: #333;">CalcPve</span><span class="p">(</span><span class="n" style="color: #333;">eval</span><span class="p">,</span> <span class="n" style="color: #333;">UtW</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">UtY_col</span><span class="p">.</span><span class="n" style="color: #333;">vector</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">l_remle_null</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">trace_G</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2738

</td>

<td class="diff-line-num new_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2741

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<pre style="margin: 0;"> <span id="LC2741" class="line" lang="cpp">                <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">pve_null</span><span class="p">,</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">pve_se_null</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2742

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<pre style="margin: 0;">+<span id="LC2742" class="line" lang="cpp">        <span class="n" style="color: #333;">debug_msg</span><span class="p">(</span><span class="s" style="color: #d14;">"main print summary"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2739

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<td class="diff-line-num new_line" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2743

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<pre style="margin: 0;"> <span id="LC2743" class="line" lang="cpp">        <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">PrintSummary</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2740

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<td class="diff-line-num new_line" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2744

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

<pre style="margin: 0;"> <span id="LC2744" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2741

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<td class="diff-line-num new_line" data-linenumber="2745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2745

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<pre style="margin: 0;"> <span id="LC2745" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// calculate and output residuals</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2771" style="width: 35px; color: rgba(0,0,0,0.3); 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="2775" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2771,15 +2775,16 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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2771

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<td class="diff-line-num new_line" data-linenumber="2775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2775

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<pre style="margin: 0;"> <span id="LC2775" class="line" lang="cpp">          <span class="n" style="color: #333;">gsl_vector_safe_free</span><span class="p">(</span><span class="n" style="color: #333;">u_hat</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2772

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<td class="diff-line-num new_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2776

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<pre style="margin: 0;"> <span id="LC2776" class="line" lang="cpp">          <span class="n" style="color: #333;">gsl_vector_safe_free</span><span class="p">(</span><span class="n" style="color: #333;">e_hat</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2773

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<td class="diff-line-num new_line" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2777

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<pre style="margin: 0;"> <span id="LC2777" class="line" lang="cpp">          <span class="n" style="color: #333;">gsl_vector_safe_free</span><span class="p">(</span><span class="n" style="color: #333;">y_hat</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2774

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<td class="diff-line-num new_line old" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2774" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2778" class="line" lang="cpp">        <span class="p">}</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// output residuals</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2775

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<td class="diff-line-num new_line" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2779

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<pre style="margin: 0;"> <span id="LC2779" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2776

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<td class="diff-line-num new_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2780

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<pre style="margin: 0;"> <span id="LC2780" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2777

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<td class="diff-line-num new_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2781

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<pre style="margin: 0;"> <span id="LC2781" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// Fit LMM or mvLMM (w. LOCO)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2778

</td>

<td class="diff-line-num new_line old" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2778" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2779

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<td class="diff-line-num new_line old" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2779" class="line" lang="cpp">          <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2782

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<pre style="margin: 0;">+<span id="LC2782" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>3</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2783" class="line" lang="cpp">          <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM9</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2780

</td>

<td class="diff-line-num new_line" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2784

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<pre style="margin: 0;"> <span id="LC2784" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">n_ph</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2785

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<pre style="margin: 0;">+<span id="LC2785" class="line" lang="cpp">          <span class="n" style="color: #333;">debug_msg</span><span class="p">(</span><span class="s" style="color: #d14;">"fit LMM (one phenotype)"</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2781

</td>

<td class="diff-line-num new_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2786

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

<pre style="margin: 0;"> <span id="LC2786" class="line" lang="cpp">          <span class="n" style="color: #333;">LMM</span> <span class="n" style="color: #333;">cLmm</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2782

</td>

<td class="diff-line-num new_line old" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2782" class="line" lang="cpp">          <span class="n" style="color: #333;">cLmm</span><span class="p">.</span><span class="n" style="color: #333;">CopyFromParam</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2787

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<pre style="margin: 0;">+<span id="LC2787" class="line" lang="cpp">          <span class="n" style="color: #333;">cLmm</span><span class="p">.</span><span class="n" style="color: #333;">CopyFromParam</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// set parameters</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2783

</td>

<td class="diff-line-num new_line" data-linenumber="2788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2788

</td>

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

<pre style="margin: 0;"> <span id="LC2788" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2784

</td>

<td class="diff-line-num new_line" data-linenumber="2789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2789

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<pre style="margin: 0;"> <span id="LC2789" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// if (is_check_mode()) disable_segfpe(); // disable fast NaN checking for now</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2785

</td>

<td class="diff-line-num new_line" data-linenumber="2790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2790

</td>

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

<pre style="margin: 0;"> <span id="LC2790" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2811" style="width: 35px; color: rgba(0,0,0,0.3); 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="2816" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2811,8 +2816,9 @@ void GEMMA::BatchRun(PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="2811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2811

</td>

<td class="diff-line-num new_line" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2816

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<pre style="margin: 0;"> <span id="LC2816" class="line" lang="cpp">          <span class="n" style="color: #333;">cLmm</span><span class="p">.</span><span class="n" style="color: #333;">WriteFiles</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2812

</td>

<td class="diff-line-num new_line" data-linenumber="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2817

</td>

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

<pre style="margin: 0;"> <span id="LC2817" class="line" lang="cpp">          <span class="n" style="color: #333;">cLmm</span><span class="p">.</span><span class="n" style="color: #333;">CopyToParam</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2813

</td>

<td class="diff-line-num new_line" data-linenumber="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2818

</td>

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

<pre style="margin: 0;"> <span id="LC2818" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2819

</td>

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

<pre style="margin: 0;">+<span id="LC2819" class="line" lang="cpp">          <span class="n" style="color: #333;">debug_msg</span><span class="p">(</span><span class="s" style="color: #d14;">"fit mvLMM (multiple phenotypes)"</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="2814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2814

</td>

<td class="diff-line-num new_line" data-linenumber="2820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2820

</td>

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

<pre style="margin: 0;"> <span id="LC2820" class="line" lang="cpp">          <span class="n" style="color: #333;">MVLMM</span> <span class="n" style="color: #333;">cMvlmm</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2815

</td>

<td class="diff-line-num new_line old" data-linenumber="2821" style="width: 35px; color: rgba(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="LC2815" class="line" lang="cpp">          <span class="n" style="color: #333;">cMvlmm</span><span class="p">.</span><span class="n" style="color: #333;">CopyFromParam</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2821

</td>

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

<pre style="margin: 0;">+<span id="LC2821" class="line" lang="cpp">          <span class="n" style="color: #333;">cMvlmm</span><span class="p">.</span><span class="n" style="color: #333;">CopyFromParam</span><span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// set parameters</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2816

</td>

<td class="diff-line-num new_line" data-linenumber="2822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2822

</td>

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

<pre style="margin: 0;"> <span id="LC2822" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2817

</td>

<td class="diff-line-num new_line" data-linenumber="2823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2823

</td>

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

<pre style="margin: 0;"> <span id="LC2823" class="line" lang="cpp">          <span class="c1" style="color: #998; font-style: italic;">// if (is_check_mode()) disable_segfpe(); // disable fast NaN checking</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2818

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<td class="diff-line-num new_line" data-linenumber="2824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2824

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<pre style="margin: 0;"> <span id="LC2824" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3377" style="width: 35px; color: rgba(0,0,0,0.3); 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="3383" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3377,7 +3383,8 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="3377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3377

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<td class="diff-line-num new_line" data-linenumber="3383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3383

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<pre style="margin: 0;"> <span id="LC3383" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3378

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<td class="diff-line-num new_line" data-linenumber="3384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3384

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<pre style="margin: 0;"> <span id="LC3384" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3379

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<td class="diff-line-num new_line" data-linenumber="3385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3385

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<pre style="margin: 0;"> <span id="LC3385" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3380

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<td class="diff-line-num new_line old" data-linenumber="3386" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3380" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3386

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<pre style="margin: 0;">+<span id="LC3386" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3387

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<pre style="margin: 0;">+<span id="LC3387" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3381

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<td class="diff-line-num new_line" data-linenumber="3388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3388

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<pre style="margin: 0;"> <span id="LC3388" class="line" lang="cpp">      <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">13</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3382

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<td class="diff-line-num new_line" data-linenumber="3389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3389

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<pre style="margin: 0;"> <span id="LC3389" class="line" lang="cpp">    <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"## REMLE log-likelihood in the null model = "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3383

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<td class="diff-line-num new_line" data-linenumber="3390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3390

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<pre style="margin: 0;"> <span id="LC3390" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">logl_remle_H0</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3546" style="width: 35px; color: rgba(0,0,0,0.3); 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="3553" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -3546,7 +3553,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPar) {</td>

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<td class="diff-line-num old_line" data-linenumber="3546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3546

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<td class="diff-line-num new_line" data-linenumber="3553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3553

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<pre style="margin: 0;"> <span id="LC3553" class="line" lang="cpp">    <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"##      time on calculating UtX = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">time_UtX</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" min "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3547

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<td class="diff-line-num new_line" data-linenumber="3554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3554

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<pre style="margin: 0;"> <span id="LC3554" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3548

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<td class="diff-line-num new_line" data-linenumber="3555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3555

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<pre style="margin: 0;"> <span id="LC3555" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3549

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<td class="diff-line-num new_line old" data-linenumber="3556" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3549" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="3556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3556" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cPar</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">||</span></span></span>

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3557

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<pre style="margin: 0;"> <span id="LC3557" class="line" lang="cpp">      <span class="p">(</span><span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">51</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">54</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="3551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3551

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<td class="diff-line-num new_line" data-linenumber="3558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3558

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<pre style="margin: 0;"> <span id="LC3558" class="line" lang="cpp">    <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"##      time on optimization = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cPar</span><span class="p">.</span><span class="n" style="color: #333;">time_opt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" min "</span></span>

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<td class="diff-line-num old_line" data-linenumber="3552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="3559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3559" class="line" lang="cpp">            <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="260f302861b2cad121d8bda95be454917dff6427">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#260f302861b2cad121d8bda95be454917dff6427"><strong>src/gemma.h</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,8 +41,10 @@ using namespace std;</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// gw:      72</span></span>

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">M_MODE</span> <span class="p">{</span> <span class="n" style="color: #333;">M_LMM1</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;">M_LMM2</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">M_LMM3</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">M_LMM4</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">M_LMM5</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">,</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp">              <span class="n" style="color: #333;">M_BSLMM5</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">15</span><span class="p">,</span></span>

</pre>

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

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp">              <span class="n" style="color: #333;">M_KIN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="n" style="color: #333;">M_KIN2</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">22</span><span class="p">,</span> <span class="n" style="color: #333;">M_EIGEN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">31</span> <span class="p">};</span></span>

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

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">  <span class="n" style="color: #333;">M_LMM9</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">9</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;">// GeneNetwork mode</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">  <span class="n" style="color: #333;">M_BSLMM5</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">15</span><span class="p">,</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">  <span class="n" style="color: #333;">M_KIN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="n" style="color: #333;">M_KIN2</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">22</span><span class="p">,</span> <span class="n" style="color: #333;">M_EIGEN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">31</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="p">};</span></span>

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

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GEMMA</span> <span class="p">{</span></span>

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

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

</pre>

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<br>

</li>

<li id="1b90beb6aa8a5b7cd88c6dee9504cb63db8a4c28">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#1b90beb6aa8a5b7cd88c6dee9504cb63db8a4c28"><strong>src/lmm.cpp</strong></a>

<hr>

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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">@@ -42,6 +42,7 @@</td>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gsl/gsl_vector.h"</span></span>

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gzstream.h"</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gemma.h"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gemma_io.h"</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "fastblas.h"</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "lapack.h"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,27 +110,28 @@ void LMM::WriteFiles() {</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">common_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">()</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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="LC112" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"beta"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"se"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">is_legacy_mode</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

118

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<td class="diff-line-num new_line old" data-linenumber="118" style="width: 35px; color: rgba(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="LC118" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"logl_H1"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span><span class="idiff left">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// we may make this an option</span></span></span>

</pre>

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

</td>

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

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM9</span></span><span class="p">)</span></span>

</pre>

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

</td>

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

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"logl_H1"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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

119

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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

<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">a_mode</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(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="LC121" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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

<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>1</span><span class="p">:</span></span>

</pre>

</td>

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

122

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

123

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

<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"l_remle"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

</pre>

</td>

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

123

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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

<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"p_wald"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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

<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

125

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<td class="diff-line-num new_line old" data-linenumber="126" style="width: 35px; color: rgba(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="LC125" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

</td>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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

<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_LMM2</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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

<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_LMM9</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

126

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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

<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"l_mle"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

129

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

<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"p_lrt"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

130

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

<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>3</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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132

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"p_score"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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131

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>4</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"l_remle"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"l_mle"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"p_wald"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,27 +144,28 @@ void LMM::WriteFiles() {</td>

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

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">sumstats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">(</span><span class="n" style="color: #333;">SUMSTAT</span> <span class="n" style="color: #333;">st</span><span class="p">)</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">scientific</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">setprecision</span><span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">beta</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">se</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"></span>

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150

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<td class="diff-line-num new_line old" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">is_legacy_mode</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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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="LC152" 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">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM9</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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

<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">logl_H1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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<td class="diff-line-num new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

154

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

153

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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

<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">a_mode</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

154

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<td class="diff-line-num new_line old" data-linenumber="156" style="width: 35px; color: rgba(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="LC154" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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

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

</td>

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

156

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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="LC156" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>1</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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

<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">lambda_remle</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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

<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">p_wald</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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

159

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

<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

158

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<td class="diff-line-num new_line old" data-linenumber="160" style="width: 35px; color: rgba(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="LC158" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

160

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

<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_LMM2</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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

<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">M_LMM9</span><span class="p">:</span></span>

</pre>

</td>

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

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

159

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

162

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

<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">lambda_mle</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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

163

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

<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">p_lrt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

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

161

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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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

<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

162

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<td class="diff-line-num new_line old" data-linenumber="165" style="width: 35px; color: rgba(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="LC162" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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

<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>3</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">p_score</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<td class="diff-line-num new_line old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;"><span class="idiff left right">M_LMM</span>4</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp">      <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">lambda_remle</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

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167

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170

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">lambda_mle</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp">              <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">st</span><span class="p">.</span><span class="n" style="color: #333;">p_wald</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,6 +176,7 @@ void LMM::WriteFiles() {</td>

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176

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

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177

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">file_gene</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp">    <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"geneID"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>

</pre>

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

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

182

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); 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="1118" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1114,7 +1118,7 @@ void LogRL_dev12(double l, void *params, double *dev1, double *dev2) {</td>

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1114

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<td class="diff-line-num new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

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<pre style="margin: 0;"> <span id="LC1118" 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="diff-line-num old_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1115

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<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1116

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<td class="diff-line-num new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1120

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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1117" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LMM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1121

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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LMM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

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<td class="diff-line-num new_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1122

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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="cpp">                     <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p_wald</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

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<td class="diff-line-num new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1123

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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_cvt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">n_cvt</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1120

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<td class="diff-line-num new_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1124

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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">n_cvt</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n_cvt</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); 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="1160" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1156,7 +1160,8 @@ void LMM::CalcRLWald(const double &l, const FUNC_PARAM &params, double &beta,</td>

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<td class="diff-line-num old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1156

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<td class="diff-line-num new_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1160

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<pre style="margin: 0;"> <span id="LC1160" 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="diff-line-num old_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1157

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<td class="diff-line-num new_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1161

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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1158

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<td class="diff-line-num new_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

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<pre style="margin: 0;"> <span id="LC1162" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1159

</td>

<td class="diff-line-num new_line old" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1159" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LMM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1163

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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1164

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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">LMM</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1160

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<td class="diff-line-num new_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1165

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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="cpp">                      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p_score</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1161

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<td class="diff-line-num new_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1166

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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_cvt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">n_cvt</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1162

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<td class="diff-line-num new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1167

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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">n_cvt</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">n_cvt</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); 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="1202" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1197,7 +1202,6 @@ void LMM::CalcRLScore(const double &l, const FUNC_PARAM &params, double &beta,</td>

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<td class="diff-line-num old_line" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1197

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<td class="diff-line-num new_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cpp">  <span class="n" style="color: #333;">gsl_matrix_free</span><span class="p">(</span><span class="n" style="color: #333;">Pab</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1198

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<td class="diff-line-num new_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="cpp">  <span class="n" style="color: #333;">gsl_vector_safe_free</span><span class="p">(</span><span class="n" style="color: #333;">Hi_eval</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1199

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<td class="diff-line-num new_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1204

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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="cpp">  <span class="n" style="color: #333;">gsl_vector_safe_free</span><span class="p">(</span><span class="n" style="color: #333;">v_temp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1200

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<td class="diff-line-num new_line old" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1200" 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="diff-line-num old_line" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1201

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<td class="diff-line-num new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1205

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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1202

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<td class="diff-line-num new_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1206

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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1203

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<td class="diff-line-num new_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1207

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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">CalcUab</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gsl_matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">UtW</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gsl_vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Uty</span><span class="p">,</span> <span class="n" style="color: #333;">gsl_matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Uab</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); 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="1422" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1418,7 +1422,7 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval,</td>

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1418

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<td class="diff-line-num new_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1422

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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="cpp">    <span class="n" style="color: #333;">CalcUab</span><span class="p">(</span><span class="n" style="color: #333;">UtW</span><span class="p">,</span> <span class="n" style="color: #333;">Uty</span><span class="p">,</span> <span class="n" style="color: #333;">Uab</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1419

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<td class="diff-line-num new_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1423

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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="cpp">    <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="n" style="color: #333;">param0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">ni_test</span><span class="p">,</span> <span class="n" style="color: #333;">n_cvt</span><span class="p">,</span> <span class="n" style="color: #333;">eval</span><span class="p">,</span> <span class="n" style="color: #333;">Uab</span><span class="p">,</span> <span class="n" style="color: #333;">ab</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1420

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<td class="diff-line-num new_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1424

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<pre style="margin: 0;"> <span id="LC1424" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1421" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

1425

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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1422

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<td class="diff-line-num new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1426

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<pre style="margin: 0;"> <span id="LC1426" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'L'</span><span class="p">,</span> <span class="n" style="color: #333;">param0</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">l_H0</span><span class="p">,</span> <span class="n" style="color: #333;">logl_H0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1423

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<td class="diff-line-num new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1427

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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1428

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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); 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="1431" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1427,16 +1431,16 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval,</td>

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<td class="diff-line-num old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1431

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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="cpp">    <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="n" style="color: #333;">param1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">ni_test</span><span class="p">,</span> <span class="n" style="color: #333;">n_cvt</span><span class="p">,</span> <span class="n" style="color: #333;">eval</span><span class="p">,</span> <span class="n" style="color: #333;">Uab</span><span class="p">,</span> <span class="n" style="color: #333;">ab</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1428

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<td class="diff-line-num new_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1432

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<pre style="margin: 0;"> <span id="LC1432" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1429

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<td class="diff-line-num new_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1433

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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// 3 is before 1.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1430

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<td class="diff-line-num new_line old" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1430" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1434

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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1431

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<td class="diff-line-num new_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1435

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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="n" style="color: #333;">l_H0</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="n" style="color: #333;">p_score</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1432

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<td class="diff-line-num new_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1436

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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1433

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<td class="diff-line-num new_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1437

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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1434

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<td class="diff-line-num new_line old" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1434" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1438

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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1435

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<td class="diff-line-num new_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1439

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<pre style="margin: 0;"> <span id="LC1439" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'R'</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">lambda_remle</span><span class="p">,</span> <span class="n" style="color: #333;">logl_H1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1436

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<td class="diff-line-num new_line" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1440

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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="n" style="color: #333;">lambda_remle</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="n" style="color: #333;">p_wald</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1437

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<td class="diff-line-num new_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1441

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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1438

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<td class="diff-line-num new_line" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1442

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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1439

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<td class="diff-line-num new_line old" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1439" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1443

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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1440

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<td class="diff-line-num new_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1444

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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp">      <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'L'</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">lambda_mle</span><span class="p">,</span> <span class="n" style="color: #333;">logl_H1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1441

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<td class="diff-line-num new_line" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1445

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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="cpp">      <span class="n" style="color: #333;">p_lrt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_cdf_chisq_Q</span><span class="p">(</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">logl_H1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">logl_H0</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1442

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<td class="diff-line-num new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1446

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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1526,17 +1530,17 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,</td>

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<td class="diff-line-num old_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1526

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<td class="diff-line-num 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">

1530

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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">logl_H1</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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<td class="diff-line-num old_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1527

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<td class="diff-line-num new_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1531

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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1528

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<td class="diff-line-num new_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1532

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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="cpp">      <span class="c1" style="color: #998; font-style: italic;">// 3 is before 1.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1529

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<td class="diff-line-num new_line old" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1529" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">4</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

1533

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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM4</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM9</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num 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">

1530

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<td class="diff-line-num new_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="cpp">        <span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="n" style="color: #333;">l_mle_null</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="n" style="color: #333;">p_score</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1531

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<td class="diff-line-num new_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1532

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<td class="diff-line-num new_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1533

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<td class="diff-line-num new_line old" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1533" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1537

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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

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<td class="diff-line-num new_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// for univariate a_mode is 1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

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<td class="diff-line-num new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1539

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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="cpp">        <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'R'</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">lambda_remle</span><span class="p">,</span> <span class="n" style="color: #333;">logl_H1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

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<td class="diff-line-num new_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1540

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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="cpp">        <span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="n" style="color: #333;">lambda_remle</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="n" style="color: #333;">p_wald</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1537

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<td class="diff-line-num new_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1538

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<td class="diff-line-num new_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1542

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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1539

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<td class="diff-line-num new_line old" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC1539" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1543

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<pre style="margin: 0;">+<span id="LC1543" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M_LMM9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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1540

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<td class="diff-line-num new_line" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1544

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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="cpp">        <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'L'</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">lambda_mle</span><span class="p">,</span> <span class="n" style="color: #333;">logl_H1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

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<td class="diff-line-num new_line" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1545

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<pre style="margin: 0;"> <span id="LC1545" class="line" lang="cpp">        <span class="n" style="color: #333;">p_lrt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_cdf_chisq_Q</span><span class="p">(</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">logl_H1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">logl_mle_H0</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1542

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<td class="diff-line-num new_line" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1546

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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1848" style="width: 35px; color: rgba(0,0,0,0.3); 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="1852" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1848,17 +1852,17 @@ void LMM::AnalyzePlink(const gsl_matrix *U, const gsl_vector *eval,</td>

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1848

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<td class="diff-line-num new_line" data-linenumber="1852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1852

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<pre style="margin: 0;"> <span id="LC1852" class="line" lang="cpp">        <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="n" style="color: #333;">param1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">ni_test</span><span class="p">,</span> <span class="n" style="color: #333;">n_cvt</span><span class="p">,</span> <span class="n" style="color: #333;">eval</span><span class="p">,</span> <span class="n" style="color: #333;">Uab</span><span class="p">,</span> <span class="n" style="color: #333;">ab</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1849

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<td class="diff-line-num new_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1853

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<pre style="margin: 0;"> <span id="LC1853" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1850

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<td class="diff-line-num new_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1854

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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// 3 is before 1, for beta.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1855" style="width: 35px; color: rgba(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="LC1851" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1855

</td>

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

<pre style="margin: 0;">+<span id="LC1855" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1852

</td>

<td class="diff-line-num new_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1856

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<pre style="margin: 0;"> <span id="LC1856" class="line" lang="cpp">          <span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="n" style="color: #333;">l_mle_null</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="n" style="color: #333;">p_score</span><span class="p">);</span></span>

</pre>

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

<td class="diff-line-num old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1853

</td>

<td class="diff-line-num new_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1857

</td>

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

<pre style="margin: 0;"> <span id="LC1857" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1854

</td>

<td class="diff-line-num new_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1858

</td>

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

<pre style="margin: 0;"> <span id="LC1858" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1855

</td>

<td class="diff-line-num new_line old" data-linenumber="1859" style="width: 35px; color: rgba(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="LC1855" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1859

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<pre style="margin: 0;">+<span id="LC1859" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1856

</td>

<td class="diff-line-num new_line" data-linenumber="1860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1860

</td>

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

<pre style="margin: 0;"> <span id="LC1860" class="line" lang="cpp">          <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'R'</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">lambda_remle</span><span class="p">,</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1857

</td>

<td class="diff-line-num new_line" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1861

</td>

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<pre style="margin: 0;"> <span id="LC1861" class="line" lang="cpp">                     <span class="n" style="color: #333;">logl_H1</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1858

</td>

<td class="diff-line-num new_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1862

</td>

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

<pre style="margin: 0;"> <span id="LC1862" class="line" lang="cpp">          <span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="n" style="color: #333;">lambda_remle</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="n" style="color: #333;">p_wald</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1859

</td>

<td class="diff-line-num new_line" data-linenumber="1863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1863

</td>

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

<pre style="margin: 0;"> <span id="LC1863" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1860

</td>

<td class="diff-line-num new_line" data-linenumber="1864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1864

</td>

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

<pre style="margin: 0;"> <span id="LC1864" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="1861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1861

</td>

<td class="diff-line-num new_line old" data-linenumber="1865" style="width: 35px; color: rgba(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="LC1861" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1865

</td>

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

<pre style="margin: 0;">+<span id="LC1865" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">M_LMM2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">M_LMM</span>4</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="1862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1862

</td>

<td class="diff-line-num new_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1866

</td>

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

<pre style="margin: 0;"> <span id="LC1866" class="line" lang="cpp">          <span class="n" style="color: #333;">CalcLambda</span><span class="p">(</span><span class="sc" style="color: #d14;">'L'</span><span class="p">,</span> <span class="n" style="color: #333;">param1</span><span class="p">,</span> <span class="n" style="color: #333;">l_min</span><span class="p">,</span> <span class="n" style="color: #333;">l_max</span><span class="p">,</span> <span class="n" style="color: #333;">n_region</span><span class="p">,</span> <span class="n" style="color: #333;">lambda_mle</span><span class="p">,</span> <span class="n" style="color: #333;">logl_H1</span><span class="p">);</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="1863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1863

</td>

<td class="diff-line-num new_line" data-linenumber="1867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1867

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<pre style="margin: 0;"> <span id="LC1867" class="line" lang="cpp">          <span class="n" style="color: #333;">p_lrt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gsl_cdf_chisq_Q</span><span class="p">(</span><span class="mf" style="color: #099;">2.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">logl_H1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">logl_mle_H0</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC1868" class="line" lang="cpp">        <span class="p">}</span></span>

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<li id="cf55255afff3a015e09fb646bb9473568ef880ef">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#cf55255afff3a015e09fb646bb9473568ef880ef"><strong>src/lmm.h</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,9 +118,9 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">gsl_vector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">env</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">WriteFiles</span><span class="p">();</span></span>

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

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CalcRLWald</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lambda</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p_wald</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CalcRLScore</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FUNC_PARAM</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">beta</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">                   <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">se</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p_score</span><span class="p">);</span></span>

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

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

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<li id="d0b2a99ae59d4e70842a1e3d7c999a4769960f74">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#d0b2a99ae59d4e70842a1e3d7c999a4769960f74"><strong>src/param.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -107,7 +107,8 @@ PARAM::PARAM(void)</td>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp">      <span class="n" style="color: #333;">time_UtZ</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">),</span> <span class="n" style="color: #333;">time_opt</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">),</span> <span class="n" style="color: #333;">time_Omega</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{}</span></span>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="n" style="color: #333;">PARAM</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">PARAM</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp">  <span class="n" style="color: #333;">gsl_rng_free</span><span class="p">(</span><span class="n" style="color: #333;">gsl_r</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gsl_r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp">    <span class="n" style="color: #333;">gsl_rng_free</span><span class="p">(</span><span class="n" style="color: #333;">gsl_r</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Read files: obtain ns_total, ng_total, ns_test, ni_test.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -510,6 +511,7 @@ void PARAM::CheckParam(void) {</td>

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<td class="diff-line-num old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

510

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp">    <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp">      <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">M_LMM9</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp">      <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">11</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">14</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp">      <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">15</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">21</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">22</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp">      <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">26</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">27</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">28</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">31</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -649,7 +651,7 @@ void PARAM::CheckParam(void) {</td>

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649

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// Only LMM option (and one prediction option) can deal with</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

650

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;">// multiple phenotypes and no gene expression files.</span></span>

</pre>

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651

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<td class="diff-line-num new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n_ph</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

652

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<td class="diff-line-num new_line old" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC652" class="line" lang="cpp">      <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">43</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

654

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp">      <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;"><span class="idiff left">9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">43</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

653

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<td class="diff-line-num new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp">    <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"error! the current analysis mode "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">a_mode</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

654

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<td class="diff-line-num new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp">         <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" can not deal with multiple phenotypes."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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655

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<td class="diff-line-num new_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp">    <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); 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="921" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -919,7 +921,7 @@ void PARAM::CheckParam(void) {</td>

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<td class="diff-line-num old_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

919

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<td class="diff-line-num new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

921

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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp">  <span class="n" style="color: #333;">enforce_fexists</span><span class="p">(</span><span class="n" style="color: #333;">file_anno</span><span class="p">,</span> <span class="s" style="color: #d14;">"open file"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

920

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<td class="diff-line-num new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

922

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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

921

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<td class="diff-line-num new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">loco</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

922

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<td class="diff-line-num new_line old" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC922" class="line" lang="cpp">    <span class="n" style="color: #333;">enforce_msg</span><span class="p">((</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">21</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">22</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

924

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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp">    <span class="n" style="color: #333;">enforce_msg</span><span class="p">((</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">21</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">22</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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<td class="diff-line-num new_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

925

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<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp">                <span class="s" style="color: #d14;">"LOCO only works with LMM and K"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

924

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<td class="diff-line-num new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

926

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<pre style="margin: 0;"> <span id="LC926" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// enforce_msg(file_bfile.empty(), "LOCO does not work with PLink (yet)");</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC927" class="line" lang="cpp">    <span class="n" style="color: #333;">enforce_msg</span><span class="p">(</span><span class="n" style="color: #333;">file_gxe</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">(),</span> <span class="s" style="color: #d14;">"LOCO does not support GXE (yet)"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -947,7 +949,7 @@ void PARAM::CheckParam(void) {</td>

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<pre style="margin: 0;"> <span id="LC949" class="line" lang="cpp">  <span class="p">}</span></span>

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948

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<td class="diff-line-num new_line" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC950" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC951" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">-<span id="LC950" class="line" lang="cpp">       <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">31</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

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<td class="diff-line-num new old_line" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp">       <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">9</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">31</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

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951

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<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp">      <span class="p">(</span><span class="n" style="color: #333;">file_kin</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">file_ku</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">file_kd</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())))</span> <span class="p">{</span></span>

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954

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<pre style="margin: 0;"> <span id="LC954" class="line" lang="cpp">    <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"error! missing relatedness file. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp">    <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<br>

</li>

<li id="609cf42db3f9cb91789592673659daf4110a98e1">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#609cf42db3f9cb91789592673659daf4110a98e1"><strong>src/param.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,7 +213,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_mh</span><span class="p">;</span>         <span class="c1" style="color: #998; font-style: italic;">// # MH steps in each iter.</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">geo_mean</span><span class="p">;</span>     <span class="c1" style="color: #998; font-style: italic;">// Mean of geometric dist.</span></span>

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<td class="diff-line-num old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">randseed</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;">// holds -seed parameter</span></span>

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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp">  <span class="n" style="color: #333;">gsl_rng</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gsl_r</span><span class="p">;</span>      <span class="c1" style="color: #998; font-style: italic;">// Track the randomizer</span></span>

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

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">  <span class="n" style="color: #333;">gsl_rng</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gsl_r</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span>      <span class="c1" style="color: #998; font-style: italic;">// Track the randomizer</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">trace_G</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cpp">  <span class="n" style="color: #333;">HYPBSLMM</span> <span class="n" style="color: #333;">cHyp_initial</span><span class="p">;</span></span>

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<li id="f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#f92b0b9f2ecd99eca4c19d9518afaae33bc2d58a"><strong>src/version.h</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// version.h generated by GEMMA scripts/gen_version_info.sh</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_VERSION "0.98.<span class="idiff left right">3</span>"</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_DATE "202<span class="idiff left right">0-11-28</span>"</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_YEAR "202<span class="idiff left right">0</span>"</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_PROFILE ""</span></span></pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_VERSION "0.98.<span class="idiff left right">4</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_DATE "202<span class="idiff left right">1-01-29</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_YEAR "202<span class="idiff left right">1</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GEMMA_PROFILE "<span class="idiff left right">/gnu/store/8mkllydvkgfy6ydlrymrx8wj0dy1x6lm-profile</span>"</span></span></pre>

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<li id="d8267812124820d08a2dfd506ddf2a9b9d0aefe9">

<a href="https://salsa.debian.org/med-team/gemma/-/compare/acf8bc6b6fa4a1c66c03107240052ed7a4298f04...8cf6fd2b71c9510451401a4767f86ad116bfdc82#d8267812124820d08a2dfd506ddf2a9b9d0aefe9"><strong>test/dev_test_suite.sh</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -82,6 +82,23 @@ testBXDLMMLikelihoodRatio() {</td>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell">    assertEquals <span class="s2" style="color: #d14;">"3088458213"</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: #000080;">-nle</span> <span class="s1" style="color: #d14;">'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }'</span> <span class="nv" style="color: #008080;">$outfn</span><span class="sb" style="color: #d14;">`</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell">testBXDLMM9LikelihoodRatio<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell">    <span class="c" style="color: #998; font-style: italic;"># Test for GeneNetwork output</span></span>

</pre>

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</td>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell">    <span class="nv" style="color: #008080;">outn</span><span class="o" style="font-weight: 600;">=</span>BXD_LMM_LR</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

</td>

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

<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell">    <span class="nv" style="color: #008080;">$gemma</span> <span class="nv" style="color: #008080;">$gemmaopts</span> <span class="nt" style="color: #000080;">-g</span> ../example/BXD_geno.txt.gz <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

</td>

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

<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell">           <span class="nt" style="color: #000080;">-p</span> ../example/BXD_pheno.txt <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

</td>

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

<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell">           <span class="nt" style="color: #000080;">-c</span> ../example/BXD_covariates2.txt <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

</td>

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

<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell">           <span class="nt" style="color: #000080;">-a</span> ../example/BXD_snps.txt <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

</td>

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

<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell">           <span class="nt" style="color: #000080;">-k</span> ./output/BXD.cXX.txt <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

</td>

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

<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell">           <span class="nt" style="color: #000080;">-lmm</span> 9 <span class="nt" style="color: #000080;">-no-check</span> <span class="nt" style="color: #000080;">-maf</span> 0.1 <span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

94

</td>

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

<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell">           <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$outn</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

</td>

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

<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell">    assertEquals 0 <span class="nv" style="color: #008080;">$?</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

</td>

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

<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

</td>

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

<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell">    <span class="nv" style="color: #008080;">outfn</span><span class="o" style="font-weight: 600;">=</span>output/<span class="nv" style="color: #008080;">$outn</span>.assoc.txt</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

</td>

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

<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell">    assertEquals <span class="s2" style="color: #d14;">"80498"</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-w</span> < <span class="nv" style="color: #008080;">$outfn</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

</td>

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

<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell">    assertEquals <span class="s2" style="color: #d14;">"3088496565"</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: #000080;">-nle</span> <span class="s1" style="color: #d14;">'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.0f",$sum }'</span> <span class="nv" style="color: #008080;">$outfn</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

100

</td>

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

<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

</td>

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

102

</td>

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="shell">testCenteredRelatednessMatrixissue188<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

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

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

86

</td>

<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

</td>

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="shell">    <span class="nv" style="color: #008080;">outn</span><span class="o" style="font-weight: 600;">=</span>issue188</span>

</pre>

</td>

</tr>

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

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

87

</td>

<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

</td>

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

<pre style="margin: 0;"> <span id="LC104" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> output/<span class="nv" style="color: #008080;">$outn</span>.<span class="k" style="font-weight: 600;">*</span></span>

</pre>

</td>

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