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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/minia">Debian Med / minia</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/8b9d8b22ca9d3b5afa018908779cbe48ce6bb3f1">8b9d8b22</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:05:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/2a4e1bfa4934679a1c20fceee3932647504a8af4">2a4e1bfa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:05:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/8b44244e6a18bd81139d8168ebad45d95a8d5968">8b44244e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:05:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/9a9b6c558164da69f55f10841749fd280e6ce395">9a9b6c55</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:05:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/b7630428d561064e1c175c1901db5cab7321172a">b7630428</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:20:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream git commit since released version is not compatible with gatb-core 1.4.1+git20191130.664696c+dfsg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/b1b6ea2d6284fe6b58350cf106bdae8b8eb2bb7b">b1b6ea2d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:21:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.1+git20191130.5b131b9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/475d757c7928931feac5868d4bb1b30b3d771a01">475d757c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:21:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.2.1+git20191130.5b131b9'
Update to upstream version '3.2.1+git20191130.5b131b9'
with Debian dir e6d9509a26fe07cf3f036bc87e3455760f03e1f3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/00301a5a7251f91a8cde9807ee2fd8c568e42258">00301a5a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-05T14:26:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Not uploaded! Just verified that building against gatb-core 1.4.1+git20191130.664696c+dfsg is OK!
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#037071f4805975493f2cb019296545ab486a120b">
merci/merci.cpp
</a>
</li>
<li class="file-stats">
<a href="#d30efc9627d8c8f9e646d5bcb3bb6c9fe6b8301d">
src/Minia.cpp
</a>
</li>
<li class="file-stats">
<a href="#7a765a4d3d79855cbebdab7b2d93e867c4406b9d">
test/ERR039477.md5
</a>
</li>
<li class="file-stats">
<a href="#bfd3439cbf4c7ae2a1f30bc68615f9f55982964d">
<span class="new-file">
+
test/bubble_covmult0.5.fa
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ cmake_minimum_required (VERSION 2.6)</td>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The default version number is the latest official build</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MAJOR 3<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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MINOR 2<span class="p">)</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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right">0</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right">1</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># But, it is possible to define another release number during a local build</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>DEFINED MAJOR<span class="p">)</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,6 +84,8 @@ link_directories (${gatb-core-extra-libraries-path})</td>
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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
84
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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>PROGRAM_SOURCE_DIR <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/src<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_RUNTIME_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/bin<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="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="cmake"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>SET CMP0009 NEW<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># fixes cmake complaining about symlinks</span></span>
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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include_directories</span> <span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROGRAM_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">file</span> <span class="p">(</span>GLOB_RECURSE ProjectFiles <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROGRAM_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/*<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ProjectFiles</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#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">@@ -2,24 +2,27 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License</span><span class="p">](</span><span class="sx" style="color: #d14;">http://img.shields.io/:license-affero-blue.svg</span><span class="p">)</span>](http://www.gnu.org/licenses/agpl-3.0.en.html)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></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="gs" style="font-weight: 600;">**Linux**</span> | <span class="gs" style="font-weight: 600;">**Mac OSX**</span> |</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">|-----------|-------------|</span>
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<pre style="margin: 0;"> <span id="LC8" 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://ci.inria.fr/gatb-core/view/Minia/job/tool-minia-build-debian7-64bits-gcc-4.7/badge/icon</span><span class="p">)</span>](https://ci.inria.fr/gatb-core/view/Minia/job/tool-minia-build-debian7-64bits-gcc-4.7/) | <span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ci.inria.fr/gatb-core/view/Minia/job/tool-minia-build-macos-10.9.5-gcc-4.2.1/badge/icon</span><span class="p">)</span>](https://ci.inria.fr/gatb-core/view/Minia/job/tool-minia-build-macos-10.9.5-gcc-4.2.1/)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">---></span>
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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="gh" style="color: #999;"># Before continuing..</span></span>
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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="LC10" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right"># What is Minia ?</span></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="idiff left right">If you are looking to do high-quality genome or metagenome assemblies, please go here: https://github.com/GATB/gatb-minia-pipeline This is a pipeline built on top of Minia that does a similar algorithm to metaSpades and MEGAHIT (multi-k assembly).</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="idiff left right">Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right"># Introduction</span></span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right"># Getting the latest source code</span></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="idiff left right">Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Back when it was released, Minia produced results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet). Now (2015 onwards), genome assemblers have evolved and in order ot have high contiguity, see the previous section. </span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#<span class="idiff left right"># Requirements</span></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="gh" style="color: #999;">#<span class="idiff left right"> Getting the latest source code</span></span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="idiff left right">CMake 2.6+; see http://www.cmake.org/cmake/resources/software.html</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">## Instructions</span></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"><span class="idiff left right">C++11 compiler; (g++ version>=4.7 (Linux), clang version>=4.3 (Mac OSX))</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="idiff left right">It is recommended to use download the latest binary release (Linux or OSX) there: https://github.com/GATB/minia/releases</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">## Instructions</span></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="idiff left right">Otherwise, Minia may be compiled from sources as follows:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # get a local copy of minia source code</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="sb" style="color: #d14;"> git clone --recursive https://github.com/GATB/minia.git</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">@@ -28,6 +31,13 @@ C++11 compiler; (g++ version>=4.7 (Linux), clang version>=4.3 (Mac OSX))</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd minia</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sh INSTALL</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Requirements</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">CMake 3.10+; see http://www.cmake.org/cmake/resources/software.html</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">C++11 compiler; (g++ version>=4.7 (Linux), clang version>=4.3 (Mac OSX))</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="gh" style="color: #999;"># User manual </span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown">Type <span class="sb" style="color: #d14;">`minia`</span> without any arguments for usage instructions.</span>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">minia (3.2.1-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">minia (3.2.1+git20191130.5b131b9-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Not uploaded! Just verified that building against</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> gatb-core 1.4.1+git20191130.664696c+dfsg is OK!</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * New upstream git commit since released version is not compatible</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> with gatb-core 1.4.1+git20191130.664696c+dfsg</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Test-Depends: bandage</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Set upstream metadata fields: Repository, Repository-Browse.</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> [ Andrius Merkys ]</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> * Adding missing copyright details for files under thirdparty/contig2fastg/.</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Andr<span class="idiff left right">ius Merkys <merkys@debian.org> Wed, 13 Nov 2019 07:06:30 -05</span>00</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- Andr<span class="idiff left right">eas Tille <tille@debian.org> Thu, 05 Dec 2019 15:25:30 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">minia (3.2.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></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">@@ -88,4 +97,3 @@ minia (1.6067+dfsg-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> * First debian package (Closes: #735158).</span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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90
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org> Sat, 21 Dec 2013 16:55:29 +0100</span></pre>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">12</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,14 +4,14 @@ Uploaders: Olivier Sallou <osallou@debian.org>,</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> bc,</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libboost-dev,</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libgatbcore-dev<span class="idiff left right"> (>= 1.4.1+git20181225.44d5a44~)</span>,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libgatbcore-dev,</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libhdf5-dev</span>
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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">
14
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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4.1</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/minia</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/minia.git</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://minia.genouest.org/</span>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: Rayan Chikhi and Guillaume Rizk</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Space-Efficient and Exact de Bruijn Graph Representation</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Based on a Bloom Filter.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Journal: Algorithms for Molecular Biology</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Year: 2013</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Volume: 8</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Number: 1</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Pages: 22</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> DOI: 10.1186/1748-7188-8-22</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> PMID: 24040893</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> URL: http://www.almob.org/content/8/1/22</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> eprint: http://minia.genouest.org/files/minia.pdf</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> <span class="idiff left right"> </span>Author: Rayan Chikhi and Guillaume Rizk</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: ></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>Space-Efficient and Exact de Bruijn Graph Representation</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Based on a Bloom Filter.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Algorithms for Molecular Biology</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2013</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 8</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 1</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 22</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1186/1748-7188-8-22</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 24040893</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://www.almob.org/content/8/1/22</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <span class="idiff left right"> </span>eprint: http://minia.genouest.org/files/minia.pdf</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Registry:</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> - Name: OMICtools</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Entry: OMICS_00022</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> - Name: bio.tools</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Entry: minia</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - Name: SciCrunch</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> Entry: SCR_004986</span></pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Name: OMICtools</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Entry: OMICS_00022</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: bio.tools</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Entry: minia</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: SciCrunch</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: SCR_004986</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Repository: https://github.com/GATB/minia</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Repository-Browse: https://github.com/GATB/minia</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">https://github.com/GATB/minia/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="mode=git,pretty=3.2.1+git%cd.%h" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/GATB/minia.git HEAD</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># Released version is not compatible with gatb-core 1.4.1+git20191130.664696c+dfsg</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># So stick to latest Git commit for the moment</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># https://github.com/GATB/minia/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#037071f4805975493f2cb019296545ab486a120b"><strong>merci/merci.cpp</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">@@ -373,6 +373,65 @@ static bool maybe_merge(uint64_t packed, connections_index_t &connections_index,</td>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"><span class="p">}</span></span>
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> </span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">parse_unitig_header</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mean_abundance</span><span class="p">)</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"><span class="p">{</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug</span><span class="p">)</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"parsing unitig links for "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">stream</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tok</span><span class="p">;</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">tok</span><span class="p">;</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" 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;">stream</span><span class="p">)</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tok</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that's the id, skip it</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tok</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"km"</span><span class="p">)</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">mean_abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">tok</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">tok</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="sc" style="color: #d14;">':'</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << "unitig " << header << " mean abundance " << mean_abundance << std::endl;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="p">}</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="p">}</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"><span class="p">}</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">renumber_glue_file</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">glue_filename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_out_tigs</span><span class="p">)</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"><span class="p">{</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="p">{</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">infile</span><span class="p">(</span><span class="n" style="color: #333;">glue_filename</span><span class="p">);</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">outfile</span><span class="p">(</span><span class="n" style="color: #333;">glue_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".tmp"</span><span class="p">);</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="p">{</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">)</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="p">{</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">space_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* // yolo</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (space_pos >= line.size())</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> {</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::cout << "error: no space in this glue file header (" << line << ") contact a developer." << std::endl;</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> exit(1);</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">end_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">space_pos</span><span class="p">);</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">new_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">nb_out_tigs</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">counter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end_header</span><span class="p">;</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" 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;">new_header</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="p">}</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" 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;">line</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="p">}</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// closes files</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">file_copy</span><span class="p">(</span><span class="n" style="color: #333;">glue_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".tmp"</span><span class="p">,</span><span class="n" style="color: #333;">glue_filename</span><span class="p">);</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">file</span><span class="p">().</span><span class="n" style="color: #333;">remove</span> <span class="p">(</span><span class="n" style="color: #333;">glue_filename</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".tmp"</span><span class="p">);</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"><span class="p">}</span></span>
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376
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"></span>
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377
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> </span>
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378
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"><span class="nf" style="color: #900; font-weight: 600;">extend_assembly_with_connections</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">assembly</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">connections_index_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">connections_index</span><span class="p">,</span> <span class="n" style="color: #333;">connections_t</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">connections</span><span class="p">,</span> <span class="n" style="color: #333;">BankFasta</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">BankFasta</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">glue</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -415,6 +474,13 @@ extend_assembly_with_connections(const string assembly, int k, int nb_threads, b</td>
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415
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474
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">getData</span><span class="p">().</span><span class="n" style="color: #333;">setRef</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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416
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475
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">_comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">lmark</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"1"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"0"</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">rmark</span><span class="o" style="font-weight: 600;">?</span><span class="s" style="color: #d14;">"1"</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"0"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//We set the sequence comment.</span></span>
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417
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">_comment</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// add coverage information </span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mean_abundance</span><span class="p">;</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_unitig_header</span><span class="p">(</span><span class="n" style="color: #333;">comment</span><span class="p">,</span><span class="n" style="color: #333;">mean_abundance</span><span class="p">);</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nb_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nb_kmers</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">_comment</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">((</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">mean_abundance</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>
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418
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> </span>
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485
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lmark</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">rmark</span><span class="p">)</span></span>
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">glue</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -438,7 +504,8 @@ void merci(int k, string reads, string assembly, int nb_threads, bool verbose)</td>
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438
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">linked_assembly</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembly</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".linked"</span><span class="p">;</span></span>
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439
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">file_copy</span><span class="p">(</span><span class="n" style="color: #333;">assembly</span><span class="p">,</span> <span class="n" style="color: #333;">linked_assembly</span><span class="p">);</span></span>
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440
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">nb_tigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span> <span class="n" style="color: #333;">linked_assembly</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">nb_tigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">renumber_unitigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// let's allow the input to be anything. Here it doesn't amtter much. We anyway renumber at the end</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span> <span class="n" style="color: #333;">linked_assembly</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">nb_tigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">);</span></span>
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442
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// real trick here</span></span>
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// tigs of length exactly k are annoying, they need to be handled carefully with UNITIG_BOTH positions</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -463,11 +530,20 @@ void merci(int k, string reads, string assembly, int nb_threads, bool verbose)</td>
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463
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"> <span class="n" style="color: #333;">glue</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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464
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> </span>
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// glue what needs to be glued. magic, we're re-using bcalm code</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"> <span class="n" style="color: #333;">bglue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span> <span class="cm" style="color: #998; font-style: italic;">/*no storage*/</span><span class="p">,</span> <span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue"</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">bglue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span> <span class="cm" style="color: #998; font-style: italic;">/*no storage*/</span><span class="p">,</span> <span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue"</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// renumber the .glue file just to avoid ID collision with .merci file</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">renumber_glue_file</span><span class="p">(</span><span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue"</span><span class="p">,</span> <span class="n" style="color: #333;">nb_tigs</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="cpp"> </span>
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// append glued to merci</span></span>
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469
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="n" style="color: #333;">file_append</span><span class="p">(</span><span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".merci"</span><span class="p">,</span> <span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".glue"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// bglue drop links so let's recreate them </span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="n" style="color: #333;">file_copy</span><span class="p">(</span><span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".merci"</span><span class="p">,</span> <span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".merci.b4link"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">renumber_unitigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// here it's absolutely mandatory to renumber if we want the output to be processed by minia</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span> <span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".merci"</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">nb_tigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">renumber_unitigs</span><span class="p">);</span></span>
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471
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"><span class="p">}</span></span>
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"></span>
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Merci</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">gatb</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">core</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">impl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Tool</span></span>
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<li id="d30efc9627d8c8f9e646d5bcb3bb6c9fe6b8301d">
<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#d30efc9627d8c8f9e646d5bcb3bb6c9fe6b8301d"><strong>src/Minia.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,8 +154,7 @@ struct MiniaFunctor { void operator () (Parameter parameter)</td>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// link contigs</span></span>
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">nb_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// doesn't matter because for now link_tigs is single-threaded</span></span>
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156
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</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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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">minia</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">minia</span><span class="p">.</span><span class="n" style="color: #333;">nbContigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">link_tigs</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">minia</span><span class="p">.</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">nb_threads</span><span class="p">,</span> <span class="n" style="color: #333;">minia</span><span class="p">.</span><span class="n" style="color: #333;">nbContigs</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>
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160
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** We gather some statistics. */</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">minia</span><span class="p">.</span><span class="n" style="color: #333;">getInfo</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">minia</span><span class="p">.</span><span class="n" style="color: #333;">getTimeInfo</span><span class="p">().</span><span class="n" style="color: #333;">getProperties</span><span class="p">(</span><span class="s" style="color: #d14;">"time"</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -274,8 +273,8 @@ string Minia::assemble (/*const, removed because Simplifications isn't const any</td>
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274
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">graphSimplifications</span><span class="p">.</span><span class="n" style="color: #333;">_bulgeLen_kAdd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDouble</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-len-kadd"</span><span class="p">);</span></span>
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275
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saw</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-altpath-kadd"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">graphSimplifications</span><span class="p">.</span><span class="n" style="color: #333;">_bulgeAltPath_kAdd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDouble</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-altpath-kadd"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saw</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-altpath-cov<span class="idiff left right">M</span>ult"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">graphSimplifications</span><span class="p">.</span><span class="n" style="color: #333;">_bulgeAltPath_covMult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDouble</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-altpath-cov<span class="idiff left right">M</span>ult"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saw</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-altpath-cov<span class="idiff left right">m</span>ult"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">graphSimplifications</span><span class="p">.</span><span class="n" style="color: #333;">_bulgeAltPath_covMult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDouble</span><span class="p">(</span><span class="s" style="color: #d14;">"-bulge-altpath-cov<span class="idiff left right">m</span>ult"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saw</span><span class="p">(</span><span class="s" style="color: #d14;">"-ec-len-kmult"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">graphSimplifications</span><span class="p">.</span><span class="n" style="color: #333;">_ecLen_kMult</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getInput</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDouble</span><span class="p">(</span><span class="s" style="color: #d14;">"-ec-len-kmult"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#7a765a4d3d79855cbebdab7b2d93e867c4406b9d"><strong>test/ERR039477.md5</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">3732560f98d63897d2b7a122938d7a42</span> # osx CI</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">037b126f9e37db1db55d23eadc40477</span>d # gcc 7 blok-bok</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">c6e5a2cf1b9c6246129ae4263da749cc</span> # debian CI</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">e92d66d1e5b7450e6f6d8f6cc1de24bf</span> # osx CI</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">3192031d3491f3488a210419c50b9d4</span>d # gcc 7 blok-bok</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">dc556ec0e91c9aad6c1a68e48a2d8456</span> # debian CI</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/compare/7a9b62aad0fbf0aaa06611704615230828ffe9ee...00301a5a7251f91a8cde9807ee2fd8c568e42258#bfd3439cbf4c7ae2a1f30bc68615f9f55982964d"><strong>test/bubble_covmult0.5.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>works well for k=21; part of genome10K.fasta</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CATCGATGCGAGACGCCTGTCGCGGGGAATTGTGGGGCGGACCACGCTCTGGCTAACGAGCTACCGTTTCCTTTAACCTGCCAGACGGTGACCAGGGCCGTTCGGCGTTGCATCGAGCGGTGTCGCTAGCGCAATGCGCAAGATTTTGACATTTACAAGGCAACATTGCAGCGTCCGATGGTCCGGTGGCCTCCAGATAGTGTCCAGTCGCTCTAACTGTATGGAGACCATAGGCATTTACCTTATTCTCATCGCCACGCCCCAAGATCTTTAGGACCCAGCATTCCTTTAACCACTAACATAACGCGTGTCATCTAGTTCAACAACC</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>that's the bubble coverage 4</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">TGTCATCTAGTTCAACAACCAAAATAACGACTCTTGCGCTCGGATGT</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>that's the bubble </span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">TGTCATCTAGTTCAACAACCAAAATAACGACTCTTGCGCTCGGATGT</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>that's the bubble </span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">TGTCATCTAGTTCAACAACCAAAATAACGACTCTTGCGCTCGGATGT</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">>that's the bubble </span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">TGTCATCTAGTTCAACAACCAAAATAACGACTCTTGCGCTCGGATGT</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>that's the bubble path 2, coverage 2</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">TGTCATCTAGTTCAACAACCAAAAAAACGACTCTTGCGCTCGGATGT</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">>that's the bubble </span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">TGTCATCTAGTTCAACAACCAAAAAAACGACTCTTGCGCTCGGATGT</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">>remaining part</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">CGACTCTTGCGCTCGGATGTCCGCAATGGGTTATCCCTATGTTCCGGTAATCTCTCATCTACTAAGCGCCCTAAAGGTCGTATGGTTGGAGGGCGGTTACACACCCTTAAGTACCGAACGATAGAGCACCCGTCTAGGAGGGCGTGCAGGGTCTCCCGCTAGCTAATGGTCACGGCCTCTCTGGGAAAGCTGAACAACGGATGATACCCATACTGCCACTCCAGTACCTGGGCCGCGTGTTGTACGCTGTGTATCTTGAGAGCGTTTCCAGCAGATAGAACAGGATCACATGTACAAA</span></pre>
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