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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/parsnp">Debian Med / parsnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/67776d1736ef2e1557d11042d0106e33d7387103">67776d17</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-16T17:39:46+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.6.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/7d682ea6c1a9d2e039c317a9ed3556c70e6c9529">7d682ea6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-16T17:39:47+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.6.1+dfsg'
Update to upstream version '1.6.1+dfsg'
with Debian dir ed045b49f022cfde39336046e909eb2eafd4a00d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/88918d90652177de6cd2d0013303ec4e8eca1ad3">88918d90</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-16T23:10:17+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.6.0 (no changes needed)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/bcf080a4b1bf021ff5b31e83696b547a93e51f8f">bcf080a4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-16T23:23:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop avoid_rpath.patch: no longer propagated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/0738b5a00fb2a74d83b705ed1f5b057c5b31e50f">0738b5a0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-16T23:23:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh, Re-diff all other patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/41828f6e417da5b1df7db81cd87b2970f547914c">41828f6e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2022-02-16T23:23:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#45167f84ef4689b3bf9ca4972093b1de3a2f5e93">
<span class="deleted-file">
−
debian/patches/avoid_rpath.patch
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<li class="file-stats">
<a href="#0c513f5715fd16df851b068e7dae0d20f44a3177">
debian/patches/blhc-fix.patch
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<li class="file-stats">
<a href="#ec411389f66e4e49fe3bf22210b81558093f9dd4">
debian/patches/drop_m64.patch
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<li class="file-stats">
<a href="#4788de9a99eb6444d4382476cd25a83234dd009d">
debian/patches/fix_build_with_as-needed.patch
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<li class="file-stats">
<a href="#5f5fd45a1541e6613ef99dd3d49ad6f1c8fe9893">
debian/patches/non-versioned-libs.patch
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<li class="file-stats">
<a href="#82bdf410ee3abb85c057e0147f43e488d2f00daf">
debian/patches/proper_calls_to_tools.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#3849e3531855982fc7f5e63b3b17488714940ae3">
parsnp
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<li class="file-stats">
<a href="#67e794015a01b8816bd16290e5f8538236da8245">
src/Makefile.am
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(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="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(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="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> </span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(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="LC5" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME == linux ]; then ./build_parsnp_linux.sh; fi</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(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="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">email</span><span class="pi">:</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">recipients</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">treangent@nbacc.net</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_success</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span></span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">on_failure</span><span class="pi">:</span> <span class="s" style="color: #d14;">change</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">os</span><span class="pi">:</span></span>
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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;">linux</span></span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,10 +51,10 @@ Recent OSX have a Gatekeeper, that's designed to ensure that only softwre from k</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Running Parsnp</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown">Parsnp can be run multiple ways, but the most common is with a set of genomes and a reference. </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown">parsnp -g <reference_genbank> -d <genomes </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown">parsnp -g <reference_genbank> -d <genomes<span class="idiff left right">></span> </span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown">parsnp -r <reference_fasta> -d <genomes </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">parsnp -r <reference_fasta> -d <genomes<span class="idiff left right">></span> </span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">For example, </span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="p">```</span></span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT(parsnp,1.<span class="idiff left right">5.3</span>)</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE(parsnp,1.<span class="idiff left right">5.3</span>)</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(parsnp,1.<span class="idiff left right">6.1</span>)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE(parsnp,1.<span class="idiff left right">6.1</span>)</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">AC_PROG_CC(gcc)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">AC_ARG_WITH(libmuscle, [ --with-libmuscle=<path/to/libmuscle> libMUSCLE install dir (default: `pwd`/muscle)])</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parsnp (1.6.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 1.6.1+dfsg</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Bump Standards-Version to 4.6.0 (no changes needed)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Drop avoid_rpath.patch: no longer propagated</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Refresh, Re-diff all other patches</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Wed, 16 Feb 2022 23:10:22 +0530</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">parsnp (1.5.6+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libmuscle-dev</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/parsnp</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/parsnp.git</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#45167f84ef4689b3bf9ca4972093b1de3a2f5e93"><strong>debian/patches/avoid_rpath.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 20 Apr 2016 10:31:32 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: There is no point in keeping rpath to a system library</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/src/Makefile.am</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.am</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> parsnp_core_CXXFLAGS = -fopenmp -O2 -m64 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize </span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -Wl,-rpath,$(libmuscle)/lib -L$(libmuscle)/lib -lMUSCLE-3.7 </span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -L$(libmuscle)/lib -lMUSCLE-3.7</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> bin_PROGRAMS = parsnp_core</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> parsnp_core_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> bindir = $(top_srcdir)/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#0c513f5715fd16df851b068e7dae0d20f44a3177"><strong>debian/patches/blhc-fix.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,8 +4,8 @@ Last-Update: 2021-05-31</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize <span class="idiff left right"> </span>-std=gnu++0x</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize <span class="idiff left right"> </span>-std=gnu++0x -D_FORTIFY_SOURCE=2</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> LIBS = -fopenmp -lstdc++ -lpthread -L$(libmuscle)/lib -lMUSCLE</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> bin_PROGRAMS = parsnp_core</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> parsnp_core_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h </span></pre>
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<li id="ec411389f66e4e49fe3bf22210b81558093f9dd4">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#ec411389f66e4e49fe3bf22210b81558093f9dd4"><strong>debian/patches/drop_m64.patch</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">@@ -12,6 +12,6 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_CXXFLAGS = -fopenmp -O2 -m64 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize </span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize </span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -L$<span class="idiff left right">(libmuscle)</span>/lib -lMUSCLE-3.7</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -L$<span class="idiff left">{CONDA_PREFIX}</span>/lib -lMUSCLE-3.7<span class="idiff right"> </span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> bin_PROGRAMS = parsnp_core</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> parsnp_core_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h </span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#4788de9a99eb6444d4382476cd25a83234dd009d"><strong>debian/patches/fix_build_with_as-needed.patch</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">@@ -9,8 +9,8 @@ Bug-Debian: https://bugs.debian.org/845415</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize </span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -L$<span class="idiff left right">(libmuscle)</span>/lib -lMUSCLE-3.7</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-parsnp_core_LDFLAGS = -fopenmp -lstdc++ -lpthread -std=gnu++0x -L$<span class="idiff left">{CONDA_PREFIX}</span>/lib -lMUSCLE-3.7<span class="idiff right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize <span class="idiff left right"> </span>-std=gnu++0x</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LIBS = -fopenmp -lstdc++ -lpthread -L$(libmuscle)/lib -lMUSCLE-3.7</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> bin_PROGRAMS = parsnp_core</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> parsnp_core_SOURCES = MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h </span>
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<li id="5f5fd45a1541e6613ef99dd3d49ad6f1c8fe9893">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#5f5fd45a1541e6613ef99dd3d49ad6f1c8fe9893"><strong>debian/patches/non-versioned-libs.patch</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">@@ -5,7 +5,7 @@ Last-Update: Wed, 18 Jul 2018 13:17:32 +0200</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/src/Makefile.am</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> parsnp_core_CXXFLAGS = -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize <span class="idiff left right"> </span>-std=gnu++0x</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIBS = -fopenmp -lstdc++ -lpthread -L$(libmuscle)/lib -lMUSCLE-3.7</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LIBS = -fopenmp -lstdc++ -lpthread -L$(libmuscle)/lib -lMUSCLE</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> bin_PROGRAMS = parsnp_core</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#82bdf410ee3abb85c057e0147f43e488d2f00daf"><strong>debian/patches/proper_calls_to_tools.patch</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">@@ -13,7 +13,7 @@ Description: Fix name of phipack executable</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> run_command(command,1)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> os.chdir(currdir)</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -60<span class="idiff left">0</span>,7 +60<span class="idiff right">0</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -60<span class="idiff left">8</span>,7 +60<span class="idiff right">8</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> # Check for dependencies</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> missing = False</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ Description: Fix name of phipack executable</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> if shutil.which(exe) is None:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> missing = True</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> logger.critical("{} not in system path!".format(exe))</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">898</span>,7 +<span class="idiff right">898</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">917</span>,7 +<span class="idiff right">917</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> if xtrafast or 1:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> extend = False</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ Description: Fix name of phipack executable</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> inifiled = inifiled.replace("$REF", ref)</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> inifiled = inifiled.replace("$EXTEND", "%d"%(extend))</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> inifiled = inifiled.replace("$ANCHORS", str(anchor))</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left">55</span>,10 +9<span class="idiff right">55</span>,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left">74</span>,10 +9<span class="idiff right">74</span>,10 @@</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> logger.info("Recruiting genomes...")</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> if use_parsnp_mumi:</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> if not inifile_exists:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +44,7 @@ Description: Fix name of phipack executable</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> run_command(command)</span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> try:</span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> mumif = open(os.path.join(outputDir, "all.mumi"),'r')</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left">61</span>,14 +11<span class="idiff right">61</span>,14 @@</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left">80</span>,14 +11<span class="idiff right">80</span>,14 @@</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> if command == "" and xtrafast and 0:</span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> command = "%s/parsnpA_fast %sparsnpAligner.ini"%(PARSNP_DIR,outputDir+os.sep)</span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> elif command == "":</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,12 +62,12 @@ Description: Fix name of phipack executable</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> run_command(command)</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> if not os.path.exists(os.path.join(outputDir, "parsnpAligner.xmfa")):</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="p">@@ -13<span class="idiff left">7</span>5,7 +13<span class="idiff right">7</span>5,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> break</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> if not use_fasttree:</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> with tempfile.TemporaryDirectory() as raxml_output_dir:</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- command = "raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"%(threads,outputDir+os.sep+"parsnp.snps.mblocks", raxml_output_dir)</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ command = "raxmlHPC -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"%(threads,outputDir+os.sep+"parsnp.snps.mblocks", raxml_output_dir)</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> run_command(command)</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> os.system("mv {}/RAxML_bestTree.OUTPUT {}".format(raxml_output_dir, outputDir+os.sep+"parsnp.tree"))</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -13<span class="idiff left">9</span>5,7 +13<span class="idiff right">9</span>5,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> <span class="idiff left right"> </span>break</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> <span class="idiff left right"> </span>if not use_fasttree:</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> <span class="idiff left right"> </span>with tempfile.TemporaryDirectory() as raxml_output_dir:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <span class="idiff left right"> </span>command = "raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"%(threads,outputDir+os.sep+"parsnp.snps.mblocks", raxml_output_dir)</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right"> </span>command = "raxmlHPC -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"%(threads,outputDir+os.sep+"parsnp.snps.mblocks", raxml_output_dir)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> <span class="idiff left right"> </span>run_command(command)</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> <span class="idiff left right"> </span>os.system("mv {}/RAxML_bestTree.OUTPUT {}".format(raxml_output_dir, outputDir+os.sep+"parsnp.tree"))</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">avoid_rpath.patch</span>
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2
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">add_missing_interpreter_line.patch</span>
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3
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">proper_calls_to_tools.patch</span>
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4
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">drop_m64.patch</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#3849e3531855982fc7f5e63b3b17488714940ae3"><strong>parsnp</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">@@ -14,7 +14,7 @@ import signal</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.<span class="idiff left right">5.6</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.<span class="idiff left right">6.1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">reroot_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="c1" style="color: #998; font-style: italic;">#use --midpoint-reroot</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -471,6 +471,14 @@ def parse_args():</td>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># help = "Enable filtering of SNPs located in PhiPack identified regions of recombination")</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">misc_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">"Misc"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">misc_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="s" style="color: #d14;">"--skip-phylogeny"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Do not generate phylogeny from core SNPs"</span><span class="p">)</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">misc_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="s" style="color: #d14;">"--validate-input"</span><span class="p">,</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Use Biopython to validate input files"</span><span class="p">)</span></span>
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">misc_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="s" style="color: #d14;">"--use-fasttree"</span><span class="p">,</span></span>
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -642,6 +650,17 @@ if __name__ == "__main__":</td>
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642
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">input_files</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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643
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651
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">critical</span><span class="p">(</span><span class="s" style="color: #d14;">"Less than 2 input sequences provided..."</span><span class="p">)</span></span>
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652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">validate_input</span><span class="p">:</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">input_files</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">([</span><span class="n" style="color: #333;">ref</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"!"</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="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"{} is an invalid sequence file!"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">records</span><span class="p">:</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"GATCRYWSMKHBVDN"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"GATCRYWSMKHBVDN"</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Genome sequence {} has invalid characters {}! Skip!"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"AGCTNagctn"</span><span class="p">)))</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"></span>
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse reference if necessary</span></span>
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647
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ref</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"!"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="832" style="width: 35px; color: rgba(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="851" style="width: 35px; color: rgba(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">@@ -832,7 +851,7 @@ SETTINGS:</td>
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832
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'-'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq</span><span class="p">:</span></span>
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833
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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834
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853
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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835
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">warning</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Genome sequence %s seems to be aligned! Skip!"</span><span class="o" style="font-weight: 600;">%</span><span class="p">((</span><span class="n" style="color: #333;">input_file</span><span class="p">)))</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">error</span></span><span class="p">(</span><span class="s" style="color: #d14;">"Genome sequence %s seems to be aligned! Skip!"</span><span class="o" style="font-weight: 600;">%</span><span class="p">((</span><span class="n" style="color: #333;">input_file</span><span class="p">)))</span></span>
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836
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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837
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">20</span><span class="p">:</span></span>
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"File %s is less than or equal to 20bp in length. Skip!"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1344" style="width: 35px; color: rgba(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">@@ -1325,7 +1344,7 @@ Please verify recruited genomes are all strain of interest""")</td>
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1325
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="python"> <span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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1326
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="python"> <span class="n" style="color: #333;">chr_spos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ref_seqs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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1327
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_seqs</span><span class="p">:</span></span>
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1328
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<pre style="margin: 0;">-<span id="LC1328" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">block_spos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chr_spos</span><span class="p">:</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">block_spos</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">chr_spos</span><span class="p"><span class="idiff right">)</span>:</span></span>
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="python"> <span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_seqs</span><span class="p">[</span><span class="n" style="color: #333;">cs</span><span class="p">]</span></span>
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1330
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<td class="new_line diff-line-num" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1349
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<pre style="margin: 0;"> <span id="LC1349" class="line" lang="python"> <span class="n" style="color: #333;">bedfile_dict</span><span class="p">[</span><span class="n" style="color: #333;">srpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">REC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.3f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">srpos</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">block_spos</span><span class="p">,</span><span class="nb" style="color: #0086b3;">eval</span><span class="p">)</span></span>
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1331
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1350
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1366" style="width: 35px; color: rgba(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="1385" style="width: 35px; color: rgba(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">@@ -1366,60 +1385,61 @@ Please verify recruited genomes are all strain of interest""")</td>
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1366
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<td class="new_line diff-line-num" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1385
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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">generate_vcf</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1367
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<td class="new_line diff-line-num" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="s" style="color: #d14;">"harvesttools -q -i %s/parsnp.ggr -V "</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.vcf"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1368
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<td class="new_line diff-line-num" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1387
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<pre style="margin: 0;"> <span id="LC1387" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1369
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1369" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Reconstructing core genome phylogeny..."</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1370
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1370" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">,</span> <span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mblocks</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1371
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1371" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mblocks</span><span class="p">:</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1372
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1372" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1373
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1373" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Not enough SNPs to use RaxML. Attempting to use FastTree instead..."</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1374
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1374" class="line" lang="python"> <span class="n" style="color: #333;">use_fasttree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1375
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1375" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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1376
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1376" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">use_fasttree</span><span class="p">:</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1377
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1377" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">TemporaryDirectory</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">raxml_output_dir</span><span class="p">:</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1378
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1378" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">,</span> <span class="n" style="color: #333;">raxml_output_dir</span><span class="p">)</span></span>
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1379
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1379" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1380
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<td class="new_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(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="LC1380" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv {}/RAxML_bestTree.OUTPUT {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">raxml_output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">skip_phylogeny</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Reconstructing core genome phylogeny..."</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">,</span> <span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">))</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">mblocks</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1391
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mblocks</span><span class="p">:</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1392
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">6</span><span class="p">:</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Not enough SNPs to use RaxML. Attempting to use FastTree instead..."</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="python"> <span class="n" style="color: #333;">use_fasttree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1395
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1396
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">use_fasttree</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">TemporaryDirectory</span><span class="p">()</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">raxml_output_dir</span><span class="p">:</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">,</span> <span class="n" style="color: #333;">raxml_output_dir</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv {}/RAxML_bestTree.OUTPUT {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">raxml_output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span><span class="p">))</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="python"> <span class="n" style="color: #333;">mblocks_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">,</span> <span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="python"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_fasttree</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">which</span><span class="p">(</span><span class="s" style="color: #d14;">"FastTreeMP"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"OMP_NUM_THREADS"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">)</span></span>
</pre>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FastTreeMP -nt -quote -gamma -slow -boot 100 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks > "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"FastTreeMP failed. Trying fasttree..."</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fasttree -nt -quote -gamma -slow -boot 100 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks > "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span></span>
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1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="python"> </span>
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1381
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="python"></span>
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1382
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<td class="new_line diff-line-num old" data-linenumber="1415" style="width: 35px; color: rgba(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="LC1382" class="line" lang="python"> <span class="n" style="color: #333;">mblocks_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">,</span> <span class="s" style="color: #d14;">"parsnp.snps.mblocks"</span><span class="p">)</span></span>
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1383
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1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="python"></span>
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1384
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<pre style="margin: 0;">-<span id="LC1384" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_fasttree</span><span class="p">:</span></span>
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1385
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<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(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="LC1385" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">which</span><span class="p">(</span><span class="s" style="color: #d14;">"FastTreeMP"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1386
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<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(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="LC1386" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">environ</span><span class="p">[</span><span class="s" style="color: #d14;">"OMP_NUM_THREADS"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">)</span></span>
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1387
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<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(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="LC1387" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"FastTreeMP -nt -quote -gamma -slow -boot 100 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks > "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span></span>
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1388
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<pre style="margin: 0;">-<span id="LC1388" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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1389
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<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(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="LC1389" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1390
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<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(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="LC1390" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"FastTreeMP failed. Trying fasttree..."</span><span class="p">)</span></span>
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1391
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<td class="new_line diff-line-num old" data-linenumber="1416" style="width: 35px; color: rgba(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="LC1391" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fasttree -nt -quote -gamma -slow -boot 100 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.snps.mblocks > "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span></span>
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1392
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<pre style="margin: 0;">-<span id="LC1392" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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1393
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<pre style="margin: 0;">-<span id="LC1393" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#7)reroot to midpoint</span></span>
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"outtree"</span><span class="p">):</span></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"outtree"</span><span class="p">)</span></span>
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1394
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="python"></span>
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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reroot_tree</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">finalfiles</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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1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="python"> <span class="n" style="color: #333;">mtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"%sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">),</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtree</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtreedata</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_string</span><span class="p">(</span><span class="n" style="color: #333;">mtreedata</span><span class="p">,</span><span class="s" style="color: #d14;">"newick"</span><span class="p">)</span></span>
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1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">reroot_at_midpoint</span><span class="p">(</span><span class="n" style="color: #333;">update_bipartitions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="python"> <span class="n" style="color: #333;">mftreef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">as_string</span><span class="p">(</span><span class="s" style="color: #d14;">'newick'</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">,</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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1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print mftreef</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.final.tree"</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">mftreef</span><span class="p">)</span></span>
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1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv %s %s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.final.tree"</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span><span class="p">))</span></span>
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1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot process {} output, skipping midpoint reroot..</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"fasttree"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">use_fasttree</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"RaxML"</span><span class="p">))</span></span>
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1395
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1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="python"></span>
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1396
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<pre style="margin: 0;">-<span id="LC1396" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#7)reroot to midpoint</span></span>
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1397
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"outtree"</span><span class="p">):</span></span>
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1398
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<pre style="margin: 0;">-<span id="LC1398" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="s" style="color: #d14;">"outtree"</span><span class="p">)</span></span>
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1399
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1436
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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="python"></span>
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1400
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reroot_tree</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">finalfiles</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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1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1402
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="python"> <span class="n" style="color: #333;">mtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"%sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">),</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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1403
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtree</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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1404
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<pre style="margin: 0;">-<span id="LC1404" class="line" lang="python"> <span class="n" style="color: #333;">mtreedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mtreedata</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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1405
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<pre style="margin: 0;">-<span id="LC1405" class="line" lang="python"> <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dendropy</span><span class="p">.</span><span class="n" style="color: #333;">Tree</span><span class="p">.</span><span class="n" style="color: #333;">get_from_string</span><span class="p">(</span><span class="n" style="color: #333;">mtreedata</span><span class="p">,</span><span class="s" style="color: #d14;">"newick"</span><span class="p">)</span></span>
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1406
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="python"> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">reroot_at_midpoint</span><span class="p">(</span><span class="n" style="color: #333;">update_bipartitions</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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1407
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="python"> <span class="n" style="color: #333;">mftreef</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">as_string</span><span class="p">(</span><span class="s" style="color: #d14;">'newick'</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">,</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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1408
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print mftreef</span></span>
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1409
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<td class="new_line diff-line-num old" data-linenumber="1437" style="width: 35px; color: rgba(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="LC1409" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.final.tree"</span><span class="p">,</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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1410
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">mftreef</span><span class="p">)</span></span>
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1411
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="python"> <span class="n" style="color: #333;">mtreef</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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1412
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<pre style="margin: 0;">-<span id="LC1412" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv %s %s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.final.tree"</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree"</span><span class="p">))</span></span>
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1413
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<pre style="margin: 0;">-<span id="LC1413" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot process {} output, skipping midpoint reroot..</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"fasttree"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">use_fasttree</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"RaxML"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="python"></span>
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1416
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="python"></span>
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1417
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<pre style="margin: 0;">-<span id="LC1417" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">use_gingr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1418
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<pre style="margin: 0;">-<span id="LC1418" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Creating Gingr input file.."</span><span class="p">)</span></span>
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1419
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<pre style="margin: 0;">-<span id="LC1419" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">xtrafast</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1420
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<pre style="margin: 0;">-<span id="LC1420" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if newick available, add</span></span>
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1421
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new flag to update branch lengths</span></span>
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1422
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="s" style="color: #d14;">"harvesttools --midpoint-reroot -u -q -i "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.ggr -o "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.ggr -n %s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree "</span><span class="p">))</span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">use_gingr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Creating Gingr input file.."</span><span class="p">)</span></span>
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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">xtrafast</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if newick available, add</span></span>
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1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new flag to update branch lengths</span></span>
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1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="s" style="color: #d14;">"harvesttools --midpoint-reroot -u -q -i "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.ggr -o "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.ggr -n %s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"parsnp.tree "</span><span class="p">))</span></span>
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1423
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1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="python"></span>
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1424
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="python"></span>
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">elapsed</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="mf" style="color: #099;">60.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1461" style="width: 35px; color: rgba(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">@@ -1441,7 +1461,7 @@ Please verify recruited genomes are all strain of interest""")</td>
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1441
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1461
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1442
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<td class="new_line diff-line-num" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1462
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<pre style="margin: 0;"> <span id="LC1462" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Parsnp finished! All output available in %s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="p">))</span></span>
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1443
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<td class="new_line diff-line-num" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1463
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<pre style="margin: 0;"> <span id="LC1463" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Validating output directory contents"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1444
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<td class="new_line diff-line-num old" data-linenumber="1464" style="width: 35px; color: rgba(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="LC1444" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="s" style="color: #d14;">"%sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">skip_phylogeny</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="s" style="color: #d14;">"%sparsnp.tree"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1445
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<td class="new_line diff-line-num" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1465
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1446
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<td class="new_line diff-line-num" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1447
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<td class="new_line diff-line-num" data-linenumber="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1467
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<pre style="margin: 0;"> <span id="LC1467" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"parsnp.tree:</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">newick format tree is missing!"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1453" style="width: 35px; color: rgba(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="1473" style="width: 35px; color: rgba(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">@@ -1453,8 +1473,8 @@ Please verify recruited genomes are all strain of interest""")</td>
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1453
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<td class="new_line diff-line-num" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1473
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<pre style="margin: 0;"> <span id="LC1473" class="line" lang="python"> <span class="n" style="color: #333;">filepres</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1454
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<td class="new_line diff-line-num" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1474
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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1455
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<td class="new_line diff-line-num" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1475
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"parsnp.xmfa:</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">XMFA formatted multi-alignment is missing"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1456
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<td class="new_line diff-line-num old" data-linenumber="1476" style="width: 35px; color: rgba(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="LC1456" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filepres</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1457
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<td class="new_line diff-line-num old" data-linenumber="1476" style="width: 35px; color: rgba(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="LC1457" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">critical</span><span class="p">(</span><span class="s" style="color: #d14;">"Output files missing, something went wrong. Check logs and relaunch or contact developers for assistance"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>if filepres != 3:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>logger.critical("Output files missing, something went wrong. Check logs and relaunch or contact developers for assistance")</span></span>
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1458
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<td class="new_line diff-line-num" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1478
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1459
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<td class="new_line diff-line-num" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1479
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%sblocks"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">)):</span></span>
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<td class="old_line diff-line-num" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1460
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<td class="new_line diff-line-num" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1480
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="s" style="color: #d14;">"%sblocks"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">outputDir</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">sep</span><span class="p">))</span></span>
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<li id="67e794015a01b8816bd16290e5f8538236da8245">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/df9582d435206b485faf935be6e3b8825f4a80f6...41828f6e417da5b1df7db81cd87b2970f547914c#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">parsnp_core_CXXFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-O2</span> <span class="nt" style="color: #000080;">-m64</span> <span class="nt" style="color: #000080;">-funroll-all-loops</span> <span class="nt" style="color: #000080;">-fomit-frame-pointer</span> <span class="nt" style="color: #000080;">-ftree-vectorize</span> </span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">parsnp_core_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-lstdc</span>++ <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu++0x <span class="nt" style="color: #000080;">-<span class="idiff left">Wl</span></span><span class="idiff">,-rpath,</span><span class="nv" style="color: #008080;"><span class="idiff">$(libmuscle)</span></span><span class="idiff">/lib </span><span class="nt" style="color: #000080;"><span class="idiff">-L</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$(libmuscle)</span></span>/lib <span class="nt" style="color: #000080;">-lMUSCLE-3</span>.7 </span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">parsnp_core_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-lstdc</span>++ <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>gnu++0x <span class="nt" style="color: #000080;">-<span class="idiff left">L</span></span><span class="nv" style="color: #008080;"><span class="idiff right">${CONDA_PREFIX}</span></span>/lib <span class="nt" style="color: #000080;">-lMUSCLE-3</span>.7 </span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">bin_PROGRAMS</span> <span class="o" style="font-weight: 600;">=</span> parsnp_core</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">parsnp_core_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> MuscleInterface.cpp MuscleInterface.h parsnp.cpp parsnp.hh LCB.cpp LCB.hh LCR.cpp LCR.hh TMum.cpp TMum.hh Converter.cpp Converter.hh ./ext/iniFile.cpp ./ext/iniFile.h </span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">bindir</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(top_srcdir)</span>/bin</span>
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