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<h3>
Julien Y. Dutheil pushed to branch master
at <a href="https://salsa.debian.org/med-team/libbpp-seq-omics">Debian Med / libbpp-seq-omics</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbpp-seq-omics/commit/f12fcff83c884f86d8892f30835763ae68db2766">f12fcff8</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-08-20T04:40:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbpp-seq-omics/commit/50b2d0b487b9c53d16e78f639c7bc50c548014f9">50b2d0b4</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-08-20T04:40:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir 61002ea6222bca9396a92fa710e29906f54e11a1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbpp-seq-omics/commit/1950286d637ac8428abd0d6a220d07869724ac13">1950286d</a></strong>
<div>
<span>by Julien Y. Dutheil</span>
<i>at 2018-08-20T07:04:55Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New version 2.4.1.
Ref: #897785
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0">
Doxyfile
</a>
</li>
<li class="file-stats">
<a href="#a6031ee51be52c563985e249b15921a89cba187e">
bpp-seq-omics.spec
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#80f394a738a146f4552f44ce90437908e264eda9">
debian/libbpp-seq-omics3.symbols
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<li class="file-stats">
<a href="#1008d43ee76137957500e95ad1aca7f08099a98b">
src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
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</li>
<li class="file-stats">
<a href="#3c1f9ff0be3b4d4a1019681d5ad1625952754502">
src/Bpp/Seq/Io/Maf/MafSequence.cpp
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</li>
<li class="file-stats">
<a href="#29489720f0c3448300689242aad729b7eece1993">
src/Bpp/Seq/Io/Maf/MafSequence.h
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</li>
<li class="file-stats">
<a href="#fdca0d5810cc177627a854a2d10f81b1303284a2">
src/Bpp/Seq/Io/Maf/MafStatistics.cpp
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</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)</td>
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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
95
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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC95" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># Packager</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
96
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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC96" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_NAME <span class="s2" style="color: #d14;">"libbpp-seq-omics"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC97" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VENDOR <span class="s2" style="color: #d14;">"Bio++ Development Team"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<td class="diff-line-num new_line old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC98" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"2.4.<span class="idiff left right">0</span>"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION <span class="s2" style="color: #d14;">"2.4.<span class="idiff left right">1</span>"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC99" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MAJOR <span class="s2" style="color: #d14;">"2"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC100" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_MINOR <span class="s2" style="color: #d14;">"4"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">0</span>"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">1</span>"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
102
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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_PACKAGE_DESCRIPTION_SUMMARY <span class="s2" style="color: #d14;">"The Bio++ Sequence-Omics library"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_LICENSE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/COPYING.txt"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CPACK_RESOURCE_FILE_AUTHORS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/AUTHORS.txt"</span><span class="p">)</span></span>
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<li id="3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#3fa7b3d8e9b1a6a923cff77497ab817d9f94b6c0"><strong>Doxyfile</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">@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-seq-omics</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"># could be handy for archiving the generated documentation or if some version</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"># control system is used.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">PROJECT_NUMBER = 2.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">PROJECT_NUMBER = 2.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"># Using the PROJECT_BRIEF tag one can provide an optional one line description</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"># for a project that appears at the top of each page and should give viewer a</span>
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<li id="a6031ee51be52c563985e249b15921a89cba187e">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#a6031ee51be52c563985e249b15921a89cba187e"><strong>bpp-seq-omics.spec</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">URL: https://github.com/BioPP/bpp-seq-omics</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Name: bpp-seq-omics</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Version: 2.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Version: 2.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Release: 1%{?dist}</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: CECILL-2.0</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vendor: The Bio++ Project</span>
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<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>
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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">@@ -84,6 +84,8 @@ rm -rf $RPM_BUILD_ROOT</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">%{_prefix}/include/*</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">%changelog</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">* Wed Aug 15 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">- Compatibility update gcc8</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">* Fri Mar 03 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">- Increased interface number</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">- Removed dynamic exceptions declarations.</span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libbpp-seq-omics (2.4.1-1) 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"> * New upstream version.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Addresses: #897785 </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"> -- Julien Dutheil <julien.dutheil@univ-montp2.fr> Mon, 20 Aug 2018 08:48:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">libbpp-seq-omics (2.4.0-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Julien Dutheil ]</span>
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<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#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">@@ -7,7 +7,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> d-shlibs (>= 0.82),</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libbpp-seq-dev (>= 2.4.<span class="idiff left right">0</span>)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libbpp-seq-dev (>= 2.4.<span class="idiff left right">1</span>)</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.1.3</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq-omics</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq-omics.git</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">@@ -18,7 +18,7 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Depends: libbpp-seq-omics3 (= ${binary:Version}),</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> libbpp-seq-dev (>= 2.4.<span class="idiff left right">0</span>)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> libbpp-seq-dev (>= 2.4.<span class="idiff left right">1</span>)</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: Bio++ Sequence library: genomics components (development files)</span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> Bio++ is a set of C++ libraries for Bioinformatics, including sequence</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> analysis, phylogenetics, molecular evolution and population genetics.</span>
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<li id="80f394a738a146f4552f44ce90437908e264eda9">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#80f394a738a146f4552f44ce90437908e264eda9"><strong>debian/libbpp-seq-omics3.symbols</strong></a>
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<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#1008d43ee76137957500e95ad1aca7f08099a98b"><strong>src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.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">@@ -60,6 +60,8 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_()</td>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlphabetTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DNA_ALPHABET</span><span class="p">.</span><span class="n" style="color: #333;">getUnknownCharacterCode</span><span class="p">();</span></span>
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61
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nr</span><span class="p">;</span></span>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumberOfSites</span><span class="p">());</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">windowSize_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"AlignmentFilterMafIterator::analyseCurrentBlock_. Block is smaller than window size: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">TextTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">));</span></span>
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63
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aln</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">missingAsGap_</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -94,8 +96,6 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_()</td>
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94
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">window_</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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95
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Init window:</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">windowSize_</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"AlignmentFilterMafIterator::analyseCurrentBlock_. Block is smaller than window size: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">TextTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">));</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">windowSize_</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nr</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">col</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aln</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</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">@@ -284,6 +284,8 @@ MafBlock* AlignmentFilter2MafIterator::analyseCurrentBlock_()</td>
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284
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AlphabetTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DNA_ALPHABET</span><span class="p">.</span><span class="n" style="color: #333;">getUnknownCharacterCode</span><span class="p">();</span></span>
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285
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nr</span><span class="p">;</span></span>
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286
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNumberOfSites</span><span class="p">());</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">windowSize_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"AlignmentFilter2MafIterator::analyseCurrentBlock_. Block is smaller than window size: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">TextTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toString</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">aln</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">missingAsGap_</span><span class="p">)</span> <span class="p">{</span></span>
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<li id="3c1f9ff0be3b4d4a1019681d5ad1625952754502">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#3c1f9ff0be3b4d4a1019681d5ad1625952754502"><strong>src/Bpp/Seq/Io/Maf/MafSequence.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -50,7 +50,7 @@ MafSequence* MafSequence::subSequence(size_t startAt, size_t length) const</td>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">subseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toString</span><span class="p">().</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">startAt</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">);</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin_</span><span class="p">;</span></span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hasCoordinates_</span><span class="p">)</span> <span class="p">{</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">in</span>t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">startAt</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_</span>t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">startAt</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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54
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<pre style="margin: 0;"> <span id="LC54" 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;">getAlphabet</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isGap</span><span class="p">(</span><span class="k" style="font-weight: 600;">operator</span><span class="p">[](</span><span class="n" style="color: #333;">i</span><span class="p">)))</span> <span class="n" style="color: #333;">begin</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="29489720f0c3448300689242aad729b7eece1993">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#29489720f0c3448300689242aad729b7eece1993"><strong>src/Bpp/Seq/Io/Maf/MafSequence.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,12 +64,12 @@ class MafSequence:</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">hasCoordinates_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">begin_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">begin_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <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;">species_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <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;">chromosome_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">strand_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">srcSize_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">size_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="idiff left right"> </span><span class="n" style="color: #333;">srcSize_</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">MafSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Alphabet</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">AlphabetTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DNA_ALPHABET</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<li id="fdca0d5810cc177627a854a2d10f81b1303284a2">
<a href="https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13#fdca0d5810cc177627a854a2d10f81b1303284a2"><strong>src/Bpp/Seq/Io/Maf/MafStatistics.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">@@ -509,7 +509,7 @@ void SequenceDiversityMafStatistics::compute(const MafBlock& block)</td>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">e1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">a1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">e2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c2</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">a2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Compute pairwise heterozigo<span class="idiff left right">c</span>ity:</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Compute pairwise heterozigo<span class="idiff left right">s</span>ity:</span></span>
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pi</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="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -517,7 +517,7 @@ void SequenceDiversityMafStatistics::compute(const MafBlock& block)</td>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getSequence</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getSequence</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">SiteContainerTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIMILARITY_<span class="idiff left right">ALL</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">SiteContainerTools</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIMILARITY_<span class="idiff left right">NOGAP</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp"> <span class="p">}</span></span>
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