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<h3>

Shayan Doust pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5">f9cdfa4a</a></strong>

<div>

<span>by Shayan Doust</span>

<i>at 2019-10-22T12:19:10Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.9</pre>

</li>

</ul>

<h4>17 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

CHANGELOG.md

</a>

</li>

<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="#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

<span class="new-file">

+

azure-pipelines.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#f4919502f59714aa98c2d5c8a78855a31c295c88">

<span class="new-file">

+

codecov.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#9cdfb0174a78cf545f65715d751a85faf6b4fb7d">

src/assembly/low_depth_remover.h

</a>

</li>

<li class="file-stats">

<a href="#2ac6fdd796300a03b489ce5273f1638558706b9b">

src/assembly/unitig_graph.cpp

</a>

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<li class="file-stats">

<a href="#5e313e600b98c0222df232774bc75f4704eb4736">

src/definitions.h

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<li class="file-stats">

<a href="#0a5ebc32983cbbe0545c162605382d3912c759ab">

src/localasm/local_assemble.cpp

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<li class="file-stats">

<a href="#37d02c00ff54f951110a0fcc23a3f12e4a4df022">

src/megahit

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</li>

<li class="file-stats">

<a href="#f7793cfdc7f6a20048a5c984102e3f3813925fa7">

src/sequence/io/binary_reader.h

</a>

</li>

<li class="file-stats">

<a href="#6489e99bf458773cca8f928c379aed6301e3fcab">

src/sequence/kmer.h

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<li class="file-stats">

<a href="#dcea69fc1e86673cdb9604c6a1d6465039ea320f">

src/sequence/sequence_package.h

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<li class="file-stats">

<a href="#d6f77d0ce49afa54e56bb49d367d20906aae6cd7">

src/sorting/base_engine.cpp

</a>

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<li class="file-stats">

<a href="#71b6758a035e048c4b26bfdfdb8cafefe1bea608">

<span class="new-file">

+

test_data/empty.fa

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<li class="file-stats">

<a href="#0f545c82baa8b6d657c489af291d8280817dbe06">

test_data/r4.fa

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</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -13,17 +13,4 @@ script:</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">sudo make install</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">megahit --test</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">megahit --test --kmin-1pass</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">megahit --test --no-hw-accel</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># Create lcov report</span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://downloads.sourceforge.net/ltp/lcov-1.14.tar.gz</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar zvxf lcov-1.14.tar.gz</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH=lcov-1.14/bin/:${PATH}</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">lcov --capture --directory . --output-file coverage.info</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">lcov --remove coverage.info '/usr/*' --output-file coverage.info</span> <span class="c1" style="color: #998; font-style: italic;"># filter system-files</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">lcov --remove coverage.info '*xxhash/*' --output-file coverage.info</span> <span class="c1" style="color: #998; font-style: italic;"># filter xxhash-files</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">lcov --remove coverage.info '*parallel_hashmap/*' --output-file coverage.info</span> <span class="c1" style="color: #998; font-style: italic;"># filter parallel-hashmap-files</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">lcov --remove coverage.info '*pprintpp/*' --output-file coverage.info</span> <span class="c1" style="color: #998; font-style: italic;"># filter pprintpp files</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">lcov --list coverage.info</span> <span class="c1" style="color: #998; font-style: italic;"># debug info</span></span>

</pre>

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28

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

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;"># Uploading report to CodeCov</span></span>

</pre>

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

29

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

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">bash <(curl -s https://codecov.io/bash) -f coverage.info || echo "Codecov did not collect coverage reports"</span></span></pre>

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

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

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

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

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">megahit --test --no-hw-accelo || echo "Codecov did not collect coverage reports"</span></span></pre>

</td>

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<br>

</li>

<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>

<hr>

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1.2.9 / 2019-10-13</span></span>

</pre>

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

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

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">-</span>   Fix segfault triggered by length-zero sequences</span>

</pre>

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

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

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">-</span>   Fix memory detection problem for some outdated MacOS versions</span>

</pre>

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

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">-</span>   Fix an incorrect assertion in unitig graph refreshing</span>

</pre>

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

</td>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">-</span>   Added <span class="sb" style="color: #d14;">`--verbose`</span> to output full log to the screen</span>

</pre>

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6

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

</pre>

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1

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

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1.2.8 / 2019-08-10</span></span>

</pre>

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

2

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

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">-</span>   Add intermediate <span class="sb" style="color: #d14;">`megahit_core_popcnt`</span> for CPUs that have ABM but not BMI2</span>

</pre>

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

3

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

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">-</span>   Allow new assembly task with <span class="sb" style="color: #d14;">`--continue`</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,9 +101,11 @@ add_custom_target(</td>

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101

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101

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cmake">        simple_test</span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cmake">        COMMAND ./megahit --test -t 2</span>

</pre>

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

103

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103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cmake">        COMMAND MEGAHIT_NUM_MERCY_FACTOR=1.5 ./megahit --test -t 4 --mem-flag 0 --no-hw-accel</span>

</pre>

</td>

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

104

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

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="cmake">        COMMAND ./megahit --test -t 2 --kmin-1pass</span>

</pre>

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

105

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

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cmake">        COMMAND rm -rf test-random && python3 <span class="idiff left right">../test_data</span>/generate_random_fasta.py > random.fa && ./megahit -r random.fa --k-list 255 --min-count 1 -o test-random</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cmake">        COMMAND ./megahit --test -t 2 --kmin-1pass<span class="idiff left right"> --prune-level 3 --prune-depth 0</span></span>

</pre>

</td>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cmake">        COMMAND rm -rf test-random && python3 <span class="si" style="color: #d14;"><span class="idiff left">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">TEST_DATA</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span>/generate_random_fasta.py > random.fa && ./megahit -r random.fa --k-list 255 --min-count 1 -o test-random</span>

</pre>

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

106

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

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cmake">        COMMAND rm -rf test-fastg && ./megahit --test -t 2 --mem-flag 2 --keep-tmp-files -o test-fastg</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cmake">        COMMAND rm -rf test-empty && ./megahit -r <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">TEST_DATA</span><span class="si" style="color: #d14;">}</span>/empty.fa -o test-empty</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cmake">        COMMAND rm -rf test-no-contig && ./megahit -r <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">TEST_DATA</span><span class="si" style="color: #d14;">}</span>/r4.fa -o test-no-contig</span>

</pre>

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

107

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cmake">        COMMAND ./megahit_toolkit contig2fastg 59 test-fastg/intermediate_contigs/k59.contigs.fa > 59.fastg</span>

</pre>

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

108

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

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cmake">        COMMAND ./megahit_toolkit readstat < test-fastg/intermediate_contigs/k59.contigs.fa</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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

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

</pre>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,9 +19,9 @@ conda install -c bioconda megahit</td>

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

19

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

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Pre-built binaries for x86_64 Linux</span></span>

</pre>

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

20

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

20

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

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

</pre>

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

21

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

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

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">wget https://github.com/voutcn/megahit/releases/download/v1.2.<span class="idiff left right">8/MEGAHIT-1.2.8</span>-Linux-x86_64-static.tar.gz</span>

</pre>

</td>

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

23

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

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>zvxf MEGAHIT-1.2.<span class="idiff left right">8</span>-Linux-x86_64-static.tar.gz</span>

</pre>

</td>

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

24

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

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>MEGAHIT-1.2.<span class="idiff left right">8</span>-Linux-x86_64-static/bin/</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">wget https://github.com/voutcn/megahit/releases/download/v1.2.<span class="idiff left right">9/MEGAHIT-1.2.9</span>-Linux-x86_64-static.tar.gz</span>

</pre>

</td>

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

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">tar </span>zvxf MEGAHIT-1.2.<span class="idiff left right">9</span>-Linux-x86_64-static.tar.gz</span>

</pre>

</td>

</tr>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>MEGAHIT-1.2.<span class="idiff left right">9</span>-Linux-x86_64-static/bin/</span>

</pre>

</td>

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

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown">./megahit <span class="nt" style="color: #000080;">--test</span>  <span class="c" style="color: #998; font-style: italic;"># run on a toy dataset</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">./megahit <span class="nt" style="color: #000080;">-1</span> MY_PE_READ_1.fq.gz <span class="nt" style="color: #000080;">-2</span> MY_PE_READ_2.fq.gz <span class="nt" style="color: #000080;">-o</span> MY_OUTPUT_DIR</span>

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

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,4 +82,4 @@ Publications</td>

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

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"><span class="gh" style="color: #999;">License</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="gh" style="color: #999;">-------</span></span>

</pre>

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

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown">This project is licensed under the GPLv3 License - see the <span class="p">[</span><span class="nv" style="color: #008080;">LICENSE</span><span class="p">](</span><span class="sx" style="color: #d14;">LICENSE</span><span class="p">)</span> file for details</span></pre>

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

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

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

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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); 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="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown">This project is licensed under the GPLv3 License - see the <span class="p">[</span><span class="nv" style="color: #008080;">LICENSE</span><span class="p">](</span><span class="sx" style="color: #d14;">LICENSE</span><span class="p">)</span> file for details</span></pre>

</td>

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</table>

<br>

</li>

<li id="40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#40ebc6823f24f296c0cd3fddd6ccda69b74ff2e4"><strong>azure-pipelines.yml</strong></a>

<hr>

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

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

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

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>

</pre>

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

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu_1604</span></span>

</pre>

</td>

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

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

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

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

</pre>

</td>

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

</td>

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

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">      <span class="na" style="color: #008080;">vmImage</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Ubuntu-16.04'</span></span>

</pre>

</td>

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

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

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

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

</pre>

</td>

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

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

</td>

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

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

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">        <span class="na" style="color: #008080;">python36</span><span class="pi">:</span></span>

</pre>

</td>

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

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

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml">          <span class="s" style="color: #d14;">python.version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.6'</span></span>

</pre>

</td>

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

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

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml">          <span class="s" style="color: #d14;">build.type</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Debug'</span></span>

</pre>

</td>

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

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

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">          <span class="na" style="color: #008080;">sanitizer</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ON'</span></span>

</pre>

</td>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml">          <span class="na" style="color: #008080;">static</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">OFF'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml">        <span class="na" style="color: #008080;">Python27</span><span class="pi">:</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml">          <span class="s" style="color: #d14;">python.version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">2.7'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml">          <span class="s" style="color: #d14;">build.type</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Release'</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml">          <span class="na" style="color: #008080;">sanitizer</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">OFF'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">          <span class="na" style="color: #008080;">static</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ON'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">task</span><span class="pi">:</span> <span class="s" style="color: #d14;">UsePythonVersion@0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml">        <span class="na" style="color: #008080;">inputs</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml">          <span class="na" style="color: #008080;">versionSpec</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">$(python.version)'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml">          <span class="na" style="color: #008080;">addToPath</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml">          <span class="s" style="color: #d14;">mkdir build</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml">          <span class="s" style="color: #d14;">cd build</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml">          <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=$(build.type) -DSANITIZER=$(sanitizer) -DSTATIC_BUILD=$(static) ..</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml">          <span class="s" style="color: #d14;">make simple_test -j `nproc`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml">        <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">test'</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml">    <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml">        <span class="na" style="color: #008080;">1013</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml">          <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-10.13</span></span>

</pre>

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml">          <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-latest</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml">    <span class="na" style="color: #008080;">pool</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml">      <span class="na" style="color: #008080;">vmImage</span><span class="pi">:</span> <span class="s" style="color: #d14;">$(image)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml">          <span class="s" style="color: #d14;">brew install cmake gcc@9 zlib bzip2</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml">        <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">dependencies'</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml">          <span class="s" style="color: #d14;">mkdir build</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml">          <span class="s" style="color: #d14;">cd build</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml">          <span class="s" style="color: #d14;">CC=gcc-9 CXX=g++-9 cmake ..</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml">          <span class="s" style="color: #d14;">make simple_test -j `sysctl -n hw.physicalcpu`</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml">        <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">test'</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">job</span><span class="pi">:</span> <span class="s" style="color: #d14;">assembly</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeoutInMinutes</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml">    <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml">        <span class="na" style="color: #008080;">codecov</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml">          <span class="s" style="color: #d14;">build.type</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Release'</span></span>

</pre>

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55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml">          <span class="na" style="color: #008080;">sanitizer</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">OFF'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml">          <span class="na" style="color: #008080;">coverage</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ON'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml">        <span class="na" style="color: #008080;">sanitize</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml">          <span class="s" style="color: #d14;">build.type</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Debug'</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml">          <span class="na" style="color: #008080;">sanitizer</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">ON'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml">          <span class="na" style="color: #008080;">coverage</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">OFF'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml">    <span class="na" style="color: #008080;">pool</span><span class="pi">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml">      <span class="na" style="color: #008080;">vmImage</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Ubuntu-16.04'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml">          <span class="s" style="color: #d14;">mkdir build</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml">          <span class="s" style="color: #d14;">cd build</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml">          <span class="s" style="color: #d14;">cmake -DCMAKE_BUILD_TYPE=$(build.type) -DSANITIZER=$(sanitizer) -DCOVERAGE=$(coverage) ..</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml">          <span class="s" style="color: #d14;">make -j `nproc`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml">          <span class="s" style="color: #d14;">make simple_test</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml">          <span class="s" style="color: #d14;">sudo make install</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml">        <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">build</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">test'</span></span>

</pre>

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

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="yaml">          <span class="s" style="color: #d14;">curl -o- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR752/007/SRR7521507/SRR7521507_1.fastq.gz | gzip -cd | head -4000000 | gzip -1 > 1.fq.gz</span></span>

</pre>

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

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="yaml">          <span class="s" style="color: #d14;">curl -o- ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR752/007/SRR7521507/SRR7521507_2.fastq.gz | gzip -cd | head -4000000 | gzip -1 > 2.fq.gz</span></span>

</pre>

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

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml">          <span class="s" style="color: #d14;">megahit --presets meta-large -1 1.fq.gz -2 2.fq.gz -m5e9 --verbose</span></span>

</pre>

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76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml">        <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">assemble'</span></span>

</pre>

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

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml">          <span class="s" style="color: #d14;">if [ $(coverage) = 'ON' ]; then</span></span>

</pre>

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

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml">            <span class="s" style="color: #d14;">wget http://downloads.sourceforge.net/ltp/lcov-1.14.tar.gz</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml">            <span class="s" style="color: #d14;">tar zvxf lcov-1.14.tar.gz</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="yaml">            <span class="s" style="color: #d14;">export PATH=lcov-1.14/bin/:${PATH}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml">            <span class="s" style="color: #d14;">lcov --capture --directory . --output-file coverage.info</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC83" class="line" lang="yaml">            <span class="s" style="color: #d14;">lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter system-files</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC84" class="line" lang="yaml">            <span class="s" style="color: #d14;">lcov --remove coverage.info '*xxhash/*' --output-file coverage.info # filter xxhash-files</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="yaml">            <span class="s" style="color: #d14;">lcov --remove coverage.info '*parallel_hashmap/*' --output-file coverage.info # filter parallel-hashmap-files</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml">            <span class="s" style="color: #d14;">lcov --remove coverage.info '*pprintpp/*' --output-file coverage.info # filter pprintpp files</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml">            <span class="s" style="color: #d14;">lcov --list coverage.info # debug info</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml">            <span class="s" style="color: #d14;">bash <(curl -s https://codecov.io/bash) -f coverage.info -t $(CODECOV_TOKEN) || echo "Codecov did not collect coverage reports"</span></span>

</pre>

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89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="yaml">          <span class="s" style="color: #d14;">fi</span></span>

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90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="yaml">        <span class="na" style="color: #008080;">displayName</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">codecov'</span></span></pre>

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<li id="f4919502f59714aa98c2d5c8a78855a31c295c88">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#f4919502f59714aa98c2d5c8a78855a31c295c88"><strong>codecov.yml</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">coverage</span><span class="pi">:</span></span>

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2

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

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3

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

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml">      <span class="na" style="color: #008080;">default</span><span class="pi">:</span></span>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml">        <span class="na" style="color: #008080;">target</span><span class="pi">:</span> <span class="s" style="color: #d14;">0%</span></span>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">    <span class="na" style="color: #008080;">project</span><span class="pi">:</span></span>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">      <span class="na" style="color: #008080;">default</span><span class="pi">:</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml">        <span class="na" style="color: #008080;">target</span><span class="pi">:</span> <span class="s" style="color: #d14;">0%</span></span></pre>

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

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<li id="9cdfb0174a78cf545f65715d751a85faf6b4fb7d">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#9cdfb0174a78cf545f65715d751a85faf6b4fb7d"><strong>src/assembly/low_depth_remover.h</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,6 +16,5 @@ bool RemoveLocalLowDepth(UnitigGraph &graph, double min_depth, uint32_t max_len,</td>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="nf" style="color: #900; font-weight: 600;">IterateLocalLowDepth</span><span class="p">(</span><span class="n" style="color: #333;">UnitigGraph</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_depth</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c">                              <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">min_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">local_width</span><span class="p">,</span></span>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">                              <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">local_ratio</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">permanent_rm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="nf" style="color: #900; font-weight: 600;">RemoveLowDepth</span><span class="p">(</span><span class="n" style="color: #333;">UnitigGraph</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">graph</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_depth</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif  // MEGAHIT_LOW_DEPTH_REMOVER_H</span></span></pre>

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<li id="2ac6fdd796300a03b489ce5273f1638558706b9b">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#2ac6fdd796300a03b489ce5273f1638558706b9b"><strong>src/assembly/unitig_graph.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">@@ -312,7 +312,6 @@ void UnitigGraph::Refresh(bool set_changed) {</td>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp">        <span class="n" style="color: #333;">next_adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NextSimplePathAdapter</span><span class="p">(</span><span class="n" style="color: #333;">next_adapter</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">next_adapter</span><span class="p">.</span><span class="n" style="color: #333;">IsValid</span><span class="p">());</span></span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">next_adapter</span><span class="p">.</span><span class="n" style="color: #333;">GetFlag</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">kDeleted</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">next_adapter</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp">        <span class="p">}</span></span>

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<li id="5e313e600b98c0222df232774bc75f4704eb4736">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#5e313e600b98c0222df232774bc75f4704eb4736"><strong>src/definitions.h</strong></a>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef PACKAGE_VERSION</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "v1.2.<span class="idiff left right">8</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "v1.2.<span class="idiff left right">9</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sdbg/sdbg_def.h"</span></span>

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<li id="0a5ebc32983cbbe0545c162605382d3912c759ab">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#0a5ebc32983cbbe0545c162605382d3912c759ab"><strong>src/localasm/local_assemble.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AssembleAndOutput</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapper</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mapper</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SeqPackage</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">read_pkg</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp">                       <span class="n" style="color: #333;">MappingResultCollector</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">result_collector</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp">                       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">local_range</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp">                       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp">                       <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">local_range</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">                       <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">LocalAsmOption</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_num_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">local_range</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">read_pkg</span><span class="p">.</span><span class="n" style="color: #333;">max_length</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">min_num_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_pkg</span><span class="p">.</span><span class="n" style="color: #333;">max_length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp">      <span class="n" style="color: #333;">local_range</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">read_pkg</span><span class="p">.</span><span class="n" style="color: #333;">max_length</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>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">  <span class="n" style="color: #333;">xinfo</span><span class="p">(</span><span class="s" style="color: #d14;">"Minimum number of reads to do local assembly: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">min_num_reads</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp">  <span class="n" style="color: #333;">Sequence</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">contig_end</span><span class="p">;</span></span>

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<br>

</li>

<li id="37d02c00ff54f951110a0fcc23a3f12e4a4df022">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#37d02c00ff54f951110a0fcc23a3f12e4a4df022"><strong>src/megahit</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">@@ -195,6 +195,7 @@ class Options:</td>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe12</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">se</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">presets</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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199

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

200

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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200

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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">log_file_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" style="width: 35px; color: rgba(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="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,6 +322,7 @@ def parse_option(argv):</td>

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321

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<td class="diff-line-num new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

322

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">                                    <span class="s" style="color: #d14;">'mem-flag='</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC323" class="line" lang="python">                                    <span class="s" style="color: #d14;">'continue'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); 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="324" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC324" class="line" lang="python">                                    <span class="s" style="color: #d14;">'version'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); 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="325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC325" class="line" lang="python">                                    <span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC326" class="line" lang="python">                                    <span class="s" style="color: #d14;">'out-prefix='</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); 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="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python">                                    <span class="s" style="color: #d14;">'presets='</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); 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="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

328

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python">                                    <span class="s" style="color: #d14;">'test'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="398" style="width: 35px; color: rgba(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="400" style="width: 35px; color: rgba(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">@@ -398,6 +400,8 @@ def parse_option(argv):</td>

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<td class="diff-line-num old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

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<td class="diff-line-num new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

400

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">option</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--version'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); 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="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

401

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">software_info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">megahit_version</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); 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="402" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC402" class="line" lang="python">            <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); 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="403" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC403" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); 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="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python">            <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

401

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<td class="diff-line-num new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

405

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'--continue'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); 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="406" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC406" class="line" lang="python">            <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">continue_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">option</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'--out-prefix'</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="591" style="width: 35px; color: rgba(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="595" style="width: 35px; color: rgba(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">@@ -591,11 +595,19 @@ def check_reads():</td>

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591

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<td class="diff-line-num new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"></span>

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592

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<td class="diff-line-num new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

596

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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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597

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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">detect_available_mem</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

594

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(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="LC594" class="line" lang="python">    <span class="n" style="color: #333;">psize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="s" style="color: #d14;">'SC_PAGE_SIZE'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

595

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(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="LC595" class="line" lang="python">    <span class="n" style="color: #333;">pcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="s" style="color: #d14;">'SC_PHYS_PAGES'</span><span class="p">)</span></span>

</pre>

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596

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(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="LC596" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">psize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">pcount</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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597

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(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="LC597" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemError</span></span>

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598

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<td class="diff-line-num new_line old" data-linenumber="598" style="width: 35px; color: rgba(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="LC598" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">psize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pcount</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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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="LC599" class="line" lang="python">        <span class="n" style="color: #333;">psize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="s" style="color: #d14;">'SC_PAGE_SIZE'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

600

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python">        <span class="n" style="color: #333;">pcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sysconf</span><span class="p">(</span><span class="s" style="color: #d14;">'SC_PHYS_PAGES'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

601

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">psize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">pcount</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

602

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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemError</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">psize</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pcount</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); 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="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">platform</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"darwin"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">popen</span><span class="p">(</span><span class="s" style="color: #d14;">"sysctl hw.memsize"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">platform</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"linux"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

</td>

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

<pre style="margin: 0;">+<span id="LC608" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">popen</span><span class="p">(</span><span class="s" style="color: #d14;">"free"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

609

</td>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

</td>

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

<pre style="margin: 0;">+<span id="LC610" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

</td>

<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

</td>

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

<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

</td>

<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

</td>

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

<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

</td>

<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

</td>

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

<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cpu_dispatch</span><span class="p">():</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="938" style="width: 35px; color: rgba(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">@@ -926,6 +938,8 @@ def merge_final(final_k):</td>

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<td class="diff-line-num old_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

926

</td>

<td class="diff-line-num new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

938

</td>

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

<pre style="margin: 0;"> <span id="LC938" class="line" lang="python"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

927

</td>

<td class="diff-line-num new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

</td>

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

<pre style="margin: 0;"> <span id="LC939" class="line" lang="python"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

928

</td>

<td class="diff-line-num new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

940

</td>

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

<pre style="margin: 0;"> <span id="LC940" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_sub_command</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

941

</td>

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

<pre style="margin: 0;">+<span id="LC941" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

942

</td>

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

<pre style="margin: 0;">+<span id="LC942" class="line" lang="python">        <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

929

</td>

<td class="diff-line-num new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

</td>

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

<pre style="margin: 0;"> <span id="LC943" class="line" lang="python">    <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

930

</td>

<td class="diff-line-num new_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

944

</td>

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

<pre style="margin: 0;"> <span id="LC944" class="line" lang="python">    <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'command </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">))</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

</td>

<td class="diff-line-num new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

</td>

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

<pre style="margin: 0;"> <span id="LC945" class="line" lang="python"></span>

</pre>

</td>

</tr>

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<br>

</li>

<li id="f7793cfdc7f6a20048a5c984102e3f3813925fa7">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#f7793cfdc7f6a20048a5c984102e3f3813925fa7"><strong>src/sequence/io/binary_reader.h</strong></a>

<hr>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,8 @@</td>

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<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">

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

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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">

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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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">BinaryReader</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">BaseSequenceReader</span> <span class="p">{</span></span>

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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">

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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">

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

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

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

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c">  <span class="n" style="color: #333;">explicit</span> <span class="n" style="color: #333;">BinaryReader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">is_</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c">  <span class="n" style="color: #333;">explicit</span> <span class="n" style="color: #333;">BinaryReader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c">      <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">is_</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">),</span> <span class="n" style="color: #333;">buf_</span><span class="p">(</span><span class="mi" style="color: #099;">120</span><span class="p">)</span> <span class="p">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_</span><span class="p">.</span><span class="n" style="color: #333;">bad</span><span class="p">())</span> <span class="p">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c">      <span class="n" style="color: #333;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">invalid_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to open file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c">    <span class="p">}</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,14 +34,14 @@ class BinaryReader : public BaseSequenceReader {</td>

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

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

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">buf_</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;">num_words</span><span class="p">)</span> <span class="p">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c">        <span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">num_words</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c">      <span class="p">}</span></span>

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

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c">      <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">bytes_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader_</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">buf_</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">num_words</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c">      <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">bytes_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader_</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">buf_</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">num_words</span><span class="p">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c">      <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bytes_read</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">num_words</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">buf_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c">      <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)(</span><span class="n" style="color: #333;">bytes_read</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c">      <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;">reverse</span><span class="p">)</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c">        <span class="n" style="color: #333;">pkg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AppendCompactSequence</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">buf_</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>

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

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c">        <span class="n" style="color: #333;">pkg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AppendCompactSequence</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">buf_</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c">        <span class="n" style="color: #333;">pkg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AppendReversedCompactSequence</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;"><span class="idiff">buf_</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c">        <span class="n" style="color: #333;">pkg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AppendReversedCompactSequence</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">buf_</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c">      <span class="n" style="color: #333;">num_bases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">read_len</span><span class="p">;</span></span>

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<br>

</li>

<li id="6489e99bf458773cca8f928c379aed6301e3fcab">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#6489e99bf458773cca8f928c379aed6301e3fcab"><strong>src/sequence/kmer.h</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,10 @@ class Kmer {</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c">  <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">word_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TWord</span><span class="p">;</span></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="c">  <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">kNumWords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NWords</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>

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

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c">  <span class="n" style="color: #333;">Kmer</span><span class="p">()</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;">memset</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">));</span> <span class="p">}</span></span>

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

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c">  <span class="n" style="color: #333;">Kmer</span><span class="p">()</span> <span class="p">{</span></span>

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

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c">    <span class="n" style="color: #333;">static_assert</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">TWord</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">NWords</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">));</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c">  <span class="p">}</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c">  <span class="n" style="color: #333;">Kmer</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Kmer</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmer</span><span class="p">)</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;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="n" style="color: #333;">kmer</span><span class="p">.</span><span class="n" style="color: #333;">data_</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">data_</span><span class="p">));</span> <span class="p">}</span></span>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="214" style="width: 35px; color: rgba(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="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -214,7 +217,7 @@ class Kmer {</td>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="nl">private:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); 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="219" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC219" class="line" lang="c">  <span class="n" style="color: #333;">word_type</span> <span class="n" style="color: #333;">data_</span><span class="p">[</span><span class="n" style="color: #333;">kNumWords</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="220" style="width: 35px; color: rgba(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="LC217" class="line" lang="c"><span class="p">}</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">__attribute__</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">packed</span></span><span class="p"><span class="idiff right">))</span>;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC220" class="line" lang="c"><span class="p">};</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"><span class="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">std</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">NumWords</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span></span>

</pre>

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<br>

</li>

<li id="dcea69fc1e86673cdb9604c6a1d6465039ea320f">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#dcea69fc1e86673cdb9604c6a1d6465039ea320f"><strong>src/sequence/sequence_package.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(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="259" style="width: 35px; color: rgba(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">@@ -259,6 +259,12 @@ class SequencePackage {</td>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AppendStringSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// Fake a sequence whose length is 1, as we need all sequences' length > 0</span></span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// to make `GetSeqID` working</span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c">      <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">fake_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"A"</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">AppendStringSequence</span><span class="p">(</span><span class="n" style="color: #333;">fake_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">fake_sequence</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c">    <span class="n" style="color: #333;">UpdateLength</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kt" style="color: #458; font-weight: 600;">ptrdiff_t</span> <span class="n" style="color: #333;">step</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="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="LC270" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">to</span><span class="p">;</span> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">step</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="267" style="width: 35px; color: rgba(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">@@ -267,7 +273,14 @@ class SequencePackage {</td>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="c">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AppendCompactSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TWord</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">rev</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// Fake a sequence whose length is 1, as we need all sequences' length > 0</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c">      <span class="c1" style="color: #998; font-style: italic;">// to make `GetSeqID` working</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c">      <span class="n" style="color: #333;">TWord</span> <span class="n" style="color: #333;">fake_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC280" class="line" lang="c">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">AppendCompactSequence</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fake_sequence</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); 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="281" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC281" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); 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="282" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC282" class="line" lang="c">    <span class="n" style="color: #333;">UpdateLength</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); 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="283" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC283" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); 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="284" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC284" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rev</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); 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="285" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC285" class="line" lang="c">      <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">rptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">DivCeiling</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">kBasesPerWord</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>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC286" class="line" lang="c">      <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">bases_in_last_word</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kBasesPerWord</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="d6f77d0ce49afa54e56bb49d367d20906aae6cd7">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#d6f77d0ce49afa54e56bb49d367d20906aae6cd7"><strong>src/sorting/base_engine.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -218,7 +218,8 @@ void BaseSequenceSortingEngine::Lv0PrepareThreadPartition() {</td>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">average</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">meta_</span><span class="p">.</span><span class="n" style="color: #333;">num_sequences</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">n_threads_</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC219" class="line" lang="cpp">    <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">seq_from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">average</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp">    <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">seq_to</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n_threads_</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">t</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;">average</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">meta_</span><span class="p">.</span><span class="n" style="color: #333;">num_sequences</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="221" style="width: 35px; color: rgba(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="LC221" class="line" lang="cpp">    <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Lv0EncodeDiffBase</span><span class="p">(</span><span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">seq_from</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC221" class="line" lang="cpp">    <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">offset_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">seq_from</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">meta_</span><span class="p">.</span><span class="n" style="color: #333;">num_sequences</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC222" class="line" lang="cpp">        <span class="n" style="color: #333;">Lv0EncodeDiffBase</span><span class="p">(</span><span class="n" style="color: #333;">meta</span><span class="p">.</span><span class="n" style="color: #333;">seq_from</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></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="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

224

</td>

<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<pre style="margin: 0;"> <span id="LC225" 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;">unsigned</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;">kNumBuckets</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>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="71b6758a035e048c4b26bfdfdb8cafefe1bea608">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#71b6758a035e048c4b26bfdfdb8cafefe1bea608"><strong>test_data/empty.fa</strong></a>

<hr>

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

</table>

<br>

</li>

<li id="0f545c82baa8b6d657c489af291d8280817dbe06">

<a href="https://salsa.debian.org/med-team/megahit/commit/f9cdfa4a0452326b2c9c514f866eaa85aacdd6e5#0f545c82baa8b6d657c489af291d8280817dbe06"><strong>test_data/r4.fa</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" id="" style="line-height: 1.6;">

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

1

</td>

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

1

</td>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">>megahit_ref_example_42_498_1:0:0_2:0:0_12b/1</span>

</pre>

</td>

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

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

2

</td>

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

2

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

</pre>

</td>

</tr>

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

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

</td>

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

3

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>1</span>

</pre>

</td>

</tr>

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

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

</td>

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

4

</td>

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

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

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