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<h3>
Étienne Mollier 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/3a7f098447a5cd743ca06604609246d2a5620ca4">3a7f0984</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:06:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.7.2+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/8a0fc34c88c4bbdc8cc71b678de6ccd6eceb09eb">8a0fc34c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:06:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/659bfba45e456b1907e3b0cc0ed71604e3c86bca">659bfba4</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:06:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.7.2+dfsg'
Update to upstream version '1.7.2+dfsg'
with Debian dir 38342d4ae14785fe32f1b42b3fe412be4a03d759</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/f0fe99f0d7b2b17f91abf39eaa1f66c40c7da63d">f0fe99f0</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:15:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh add_missing_interpreter_line.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/99a8a9ef8b1a8b1701e9c6ba2c5ff3d86eb29cbb">99a8a9ef</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:18:44+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh proper_calls_to_tools.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/200abf1d4164bcd70aff77d28512692c760abb0f">200abf1d</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:19:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/5daa7ba63ad7035f3a3e9da4e3381308fc65fd88">5daa7ba6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:21:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/e11c5a60c37cb05064156ae19eb18a1078cf6ad0">e11c5a60</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:55:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/install,py3-parsnp-libs.patch: provide extend and logger modules
This fixes failures to import modules extend and logger.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/9fae160cafc375d95af851396cf964e456fd2f0d">9fae160c</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T16:55:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: parsnp depends on python3-biopython
This fixes failure to import Bio modules.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/a9093b483a06cc53b6a16d230be19b723c7cd395">a9093b48</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T17:06:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/parsnp.1: refresh the manual page; document new options
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/d39d82d93c0c6de0a0eae146b6b50bd16bfcb0ba">d39d82d9</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T17:17:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add typos.patch: fix typos caught by lintian.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/ca0f9296e126cd1de30793cc0a35d70f7f6bb834">ca0f9296</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-04-14T17:22:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
</a>
</li>
<li class="file-stats">
<a href="#1d48839c4a5f6c529c6b127a422dc21598760fb5">
debian/parsnp.1
</a>
</li>
<li class="file-stats">
<a href="#a5fc4131bf2a5e0bc81dac48c1b75b3a63615923">
debian/patches/add_missing_interpreter_line.patch
</a>
</li>
<li class="file-stats">
<a href="#82bdf410ee3abb85c057e0147f43e488d2f00daf">
debian/patches/proper_calls_to_tools.patch
</a>
</li>
<li class="file-stats">
<a href="#fe66df4ea9cdddb02aec648381ccad353a2bbc7b">
<span class="new-file">
+
debian/patches/py3-parsnp-libs.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e0ece4a919b15a75c23178e379a8ca9c0870bb37">
<span class="new-file">
+
debian/patches/typos.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#4d78e2d331321dd601d74ba16541706aaebecb52">
<span class="new-file">
+
extend.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#ea7cb5eaec19ba9bd46df58c8e1a23cc5da4247c">
<span class="new-file">
+
logger.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#3849e3531855982fc7f5e63b3b17488714940ae3">
parsnp
</a>
</li>
<li class="file-stats">
<a href="#ee78169a89b940136b8c2936e3018e3d83272ed7">
src/parsnp.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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1
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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC1" class="line" lang="plaintext">AC_INIT(parsnp<span class="idiff left right deletion">,</span>1.6.1)</span>
</pre></td>
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2
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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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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="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE(<span class="idiff left right deletion">parsnp,1.6.1</span>)</span>
</pre></td>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(<span class="idiff left addition">[</span>parsnp<span class="idiff addition">],[</span>1.6.1<span class="idiff right addition">]</span>)</span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AM_INIT_AUTOMAKE(<span class="idiff left right addition">[-Wall]</span>)</span>
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3
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">AC_PROG_CC(gcc)</span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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5
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parsnp (1.7.2+dfsg-1) unstable; urgency=medium</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 1.7.2+dfsg</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Refresh add_missing_interpreter_line.patch</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Refresh proper_calls_to_tools.patch</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/install,py3-parsnp-libs.patch: provide "extend" and "logger" modules;</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> this fixes failures to import said modules when running parsnp.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * d/control: parsnp depends on python3-biopython; this fixes failure to</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> import Bio modules when running parsnp.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * d/parsnp.1: refresh the manual page; document new options.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Add typos.patch: fix typos caught by lintian.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Thu, 14 Apr 2022 17:22:39 +0200</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">parsnp (1.6.2+dfsg-1) unstable; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#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">@@ -20,6 +20,7 @@ Architecture: any</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${python3:Depends},</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-biopython,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> python3-numpy,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> fasttree,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> harvest-tools,</span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">parsnp usr/bin</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">src/parsnp_core usr/lib/parsnp</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">template.ini usr/share/parsnp</span></pre></td>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#1d48839c4a5f6c529c6b127a422dc21598760fb5"><strong>debian/parsnp.1</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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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="LC2" class="line" lang="plaintext">.TH PARSNP "1" "<span class="idiff left deletion">May</span> 202<span class="idiff right deletion">1</span>" "parsnp 1.5.4" "User Commands"</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PARSNP "1" "<span class="idiff left addition">April</span> 202<span class="idiff right addition">2</span>" "parsnp 1.5.4" "User Commands"</span>
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3
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">parsnp \- rapid core genome multi-alignment</span>
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</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">@@ -94,9 +94,28 @@ Maximal diagonal difference. Either percentage (e.g. 0.2) or bp (e.g. 100bp)</td>
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94
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">Alignment program to use</span>
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95
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95
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">.TP</span>
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96
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96
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">\fB\-u\fR, \fB\-\-unaligned\fR</span>
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97
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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="LC97" class="line" lang="plaintext">Ouput unaligned regions</span>
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97
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">Output unaligned regions</span>
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98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.SS "LCB Extensions:"</span>
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99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.TP</span>
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100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-\-extend\-lcbs\fR</span>
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101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Extend the boundaries of LCBs with an ungapped alignment</span>
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102
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.TP</span>
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103
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">\fB\-\-match\-score\fR MATCH_SCORE</span>
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104
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">Value of match score for extension</span>
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105
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">.TP</span>
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106
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">\fB\-\-mismatch\-penalty MISMATCH_PENALTY</span>
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107
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">Value of mismatch score for extension (should be negative)</span>
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108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.TP</span>
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109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">\fB\-\-gap\-penalty GAP_PENALTY</span>
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110
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">Value of gap penalty for extension (should be negative)</span>
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98
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111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">.SS "Misc:"</span>
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99
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">.TP</span>
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113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">\fB\-\-skip\-phylogeny\fR</span>
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114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">Do not generate phylogeny from core SNPs</span>
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115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.TP</span>
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116
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">\fB\-\-validate\-input\fR</span>
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117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">Use Biopython to validate input files</span>
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118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.TP</span>
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100
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119
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">\fB\-\-use\-fasttree\fR</span>
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101
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120
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">Use fasttree instead of RaxML</span>
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102
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121
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">.TP</span>
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<li id="a5fc4131bf2a5e0bc81dac48c1b75b3a63615923">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#a5fc4131bf2a5e0bc81dac48c1b75b3a63615923"><strong>debian/patches/add_missing_interpreter_line.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,11 +2,11 @@ Author: Nilesh Patra</td>
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-09-21 15:59:19 +0000</span></span>
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Force Python3 interpreter</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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5
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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="LC5" class="line" lang="diff">--- <span class="idiff left right deletion">a</span>/parsnp</span>
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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="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right deletion">b</span>/parsnp</span></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right addition">parsnp.orig</span>/parsnp</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right addition">parsnp</span>/parsnp</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> # See the LICENSE file included with this software for license information.</span>
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11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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12
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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="LC12" class="line" lang="diff"> import os, sys, string, getopt, random,subprocess, time,<span class="idiff left right deletion"> glob,</span>operator, math, datetime,numpy #pysam</span></pre></td>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import os, sys, string, getopt, random,subprocess, time,operator, math, datetime,numpy #pysam</span></pre></td>
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<li id="82bdf410ee3abb85c057e0147f43e488d2f00daf">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#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">@@ -2,9 +2,9 @@ Author: Nilesh Patra</td>
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-09-21 15:59:19 +0000</span></span>
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Fix name of phipack executable</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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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="LC5" class="line" lang="diff">--- <span class="idiff left right deletion">a</span>/parsnp</span>
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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="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right deletion">b</span>/parsnp</span></span>
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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="LC7" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left deletion">86</span>,7 +1<span class="idiff right deletion">86</span>,7 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right addition">parsnp.orig</span>/parsnp</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right addition">parsnp</span>/parsnp</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left addition">37</span>,7 +1<span class="idiff right addition">37</span>,7 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> def run_phipack(query,seqlen,workingdir):</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> currdir = os.getcwd()</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> os.chdir(workingdir)</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">@@ -13,7 +13,7 @@ Description: Fix name of phipack executable</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> run_command(command,1)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> os.chdir(currdir)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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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="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left deletion">60</span>8,7 +<span class="idiff right deletion">60</span>8,7 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left addition">57</span>8,7 +<span class="idiff right addition">57</span>8,7 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> # Check for dependencies</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> if shutil.which(exe) is None:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> missing = True</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> logger.critical("{} not in system path!".format(exe))</span>
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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="LC25" class="line" lang="diff"><span class="p">@@ -<span class="idiff left deletion">917</span>,7 +<span class="idiff right deletion">917</span>,7 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -<span class="idiff left addition">894</span>,7 +<span class="idiff right addition">894</span>,7 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> if xtrafast or 1:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> extend = False</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </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">@@ -31,7 +31,7 @@ Description: Fix name of phipack executable</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> inifiled = inifiled.replace("$REF", ref)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> inifiled = inifiled.replace("$EXTEND", "%d"%(extend))</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> inifiled = inifiled.replace("$ANCHORS", str(anchor))</span>
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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="LC34" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left deletion">74</span>,10 +9<span class="idiff right deletion">74</span>,10 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -9<span class="idiff left addition">51</span>,10 +9<span class="idiff right addition">51</span>,10 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> logger.info("Recruiting genomes...")</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> if use_parsnp_mumi:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> if not inifile_exists:</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">@@ -44,7 +44,7 @@ Description: Fix name of phipack executable</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> run_command(command)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> try:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left deletion">80</span>,14 +11<span class="idiff right deletion">80</span>,14 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left addition">57</span>,14 +11<span class="idiff right addition">57</span>,14 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> if command == "" and xtrafast and 0:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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">@@ -62,10 +62,10 @@ Description: Fix name of phipack executable</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> run_command(command)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left deletion">395</span>,7 +1<span class="idiff right deletion">395</span>,7 @@</span></span>
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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="LC66" class="line" lang="diff"> <span class="idiff left right deletion"> </span>break</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left addition">409</span>,7 +1<span class="idiff right addition">409</span>,7 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> if not use_fasttree:</span>
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68
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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="LC68" class="line" lang="diff"> with <span class="idiff left right deletion">tempfile.</span>TemporaryDirectory() as raxml_output_dir:</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> with TemporaryDirectory() as raxml_output_dir:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> run_command(command)</span>
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<li id="fe66df4ea9cdddb02aec648381ccad353a2bbc7b">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#fe66df4ea9cdddb02aec648381ccad353a2bbc7b"><strong>debian/patches/py3-parsnp-libs.patch</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fetch extend.py and logger.py helpers from parsnp namespace</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This fixes failures to import logger and extend when running parsnp. This</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> patch comes along with installing the missing helpers in dist-packages/parsnp.</span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2022-04-14</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">---</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- parsnp.orig/extend.py</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ parsnp/extend.py</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import numpy as np</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> from Bio.AlignIO.MafIO import MafWriter, MafIterator</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> from Bio.AlignIO.MauveIO import MauveWriter</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from logger import logger</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- parsnp.orig/parsnp</span></span>
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21
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26
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> import multiprocessing</span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> import signal</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> __version__ = "1.7.2"</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> reroot_tree = True #use --midpoint-reroot</span></pre></td>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -4,3 +4,5 @@ drop_m64.patch</td>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">fix_build_with_as-needed.patch</span>
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5
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">non-versioned-libs.patch</span>
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">blhc-fix.patch</span>
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8
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#e0ece4a919b15a75c23178e379a8ca9c0870bb37"><strong>debian/patches/typos.patch</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix typos caught by lintian</span></span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/marbl/parsnp/pull/110</span></span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2022-04-14</span></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- parsnp.orig/parsnp</span></span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ parsnp/parsnp</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -411,7 +411,7 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> "-u",</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> "--unaligned",</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> action = "store_true",</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- help = "Ouput unaligned regions")</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> recombination_args = parser.add_argument_group("Recombination filtration")</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> #TODO -x was a duplicate flag but no longer parsed as filter-phipack-snps in the current parsnp version</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- parsnp.orig/src/parsnp.cpp</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> dif = difftime (tend,tstart);</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> cerr << "Parsnp: Finished core genome alignment" << endl;</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf(" See log file for futher details. Total processing time: %.0lf seconds \n\n", dif );</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf(" See log file for further details. Total processing time: %.0lf seconds \n\n", dif );</span></span>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#4d78e2d331321dd601d74ba16541706aaebecb52"><strong>extend.py</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="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;">AlignIO</span><span class="p">,</span> <span class="n" style="color: #333;">SeqIO</span></span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqIO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">glob</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">glob</span></span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">namedtuple</span><span class="p">,</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">,</span> <span class="n" style="color: #333;">Counter</span></span>
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">substitution_matrices</span></span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">product</span><span class="p">,</span> <span class="n" style="color: #333;">combinations</span></span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.AlignIO.MafIO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MafWriter</span><span class="p">,</span> <span class="n" style="color: #333;">MafIterator</span></span>
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.AlignIO.MauveIO</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MauveWriter</span></span>
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16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">logger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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17
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_sequence_data</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_files</span><span class="p">,</span> <span class="n" style="color: #333;">index_files</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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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">fname_to_seqrecord</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigidx_to_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fasta_f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">reference</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sequence_files</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">fasta_f</span><span class="p">).</span><span class="n" style="color: #333;">name</span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index_files</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">fname_to_seqrecord</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">]</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;">index</span><span class="p">(</span><span class="n" style="color: #333;">fasta_f</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig_id</span><span class="p">,</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fname_to_seqrecord</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">].</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ctg_idx</span><span class="p">,</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</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;">fasta_f</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idx</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigidx_to_header</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">ctg_idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigidx_to_header</span><span class="p">,</span> <span class="n" style="color: #333;">fname_to_seqrecord</span><span class="p">,</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span></span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#%%</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Writes the parsnp output to a MAF file containing. While there are methods</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># in HarvestTools that do this, they don't account for multiple contigs,</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># which is a future addition we would like to have.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">xmfa_to_maf</span><span class="p">(</span><span class="n" style="color: #333;">xmfa_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_maf_file</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigidx_to_header</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">):</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">index_to_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Avoid loading the whole alignment in memory</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="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;">xmfa_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">parsnp_fd</span><span class="p">,</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">SpooledTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta_out</span><span class="p">:</span></span>
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47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="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="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <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;">parsnp_fd</span><span class="p">):</span></span>
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48
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="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;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"##"</span><span class="p">:</span></span>
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49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" 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="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"##SequenceIndex"</span><span class="p">):</span></span>
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50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">line</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>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"##SequenceFile"</span><span class="p">):</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">line</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="n" style="color: #333;">name</span></span>
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53
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">index_to_fname</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span></span>
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54
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</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="p">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+</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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56
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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57
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_seqs</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;">fasta_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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58
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59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">curr_cluster_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">curr_cluster_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="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;">output_maf_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">maf_out</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MafWriter</span><span class="p">(</span><span class="n" style="color: #333;">maf_out</span><span class="p">)</span></span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write_header</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">header_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"^\s?(\d+):(\d+)-(\d+)\s+([+,-])\s+cluster(\d+)\s+s?(\d+)?:p(\d+)"</span><span class="p">)</span></span>
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66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Stores coordinates of aligned regions on the FORWARD strand</span></span>
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">fname_to_contigid_to_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seqrecord</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">xmfa_seqs</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">full_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="n" style="color: #333;">description</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_parser</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">full_header</span><span class="p">).</span><span class="n" style="color: #333;">groups</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">file_idx</span><span class="p">,</span> <span class="n" style="color: #333;">gstart</span><span class="p">,</span> <span class="n" style="color: #333;">gend</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">contig_idx</span><span class="p">,</span> <span class="n" style="color: #333;">position_in_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">groups</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">cluster_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cluster_idx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">curr_cluster_idx</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="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;">curr_cluster_seqs</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="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" 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;">output_maf_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">maf_out</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MafWriter</span><span class="p">(</span><span class="n" style="color: #333;">maf_out</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">msa_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span><span class="p">(</span><span class="n" style="color: #333;">curr_cluster_seqs</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">msa_record</span><span class="p">.</span><span class="n" style="color: #333;">_annotations</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"pass"</span><span class="p">:</span> <span class="n" style="color: #333;">curr_cluster_idx</span><span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write_alignment</span><span class="p">(</span><span class="n" style="color: #333;">msa_record</span><span class="p">)</span></span>
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81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">curr_cluster_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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82
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">curr_cluster_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_idx</span></span>
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83
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="python"></span>
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84
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There are some Parsnp indexing situations that need to be corrected.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC85" class="line" lang="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;">contig_idx</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">contig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">start_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">position_in_contig</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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88
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC88" 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="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">start_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">position_in_contig</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">contig_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">contig_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">file_idx</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">contig_idx</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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92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">start_coord</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>
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93
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94
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add annotations to the seqrecord in order to pass to mafwriter</span></span>
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95
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index_to_fname</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">file_idx</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">contig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_contigidx_to_header</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_idx</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">src_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="n" style="color: #333;">seq</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="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">:<-file:contig->:</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">contig_id</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"srcSize"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_size</span></span>
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102
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"size"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span></span>
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103
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parsnp coordinates are always on the fwd strand, even for revcomp hits</span></span>
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104
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># we adjust for that here</span></span>
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105
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">seqrecord</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_coord</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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="n" style="color: #333;">src_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start_coord</span></span>
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106
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">curr_cluster_seqs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqrecord</span><span class="p">)</span></span>
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107
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># In order to keep track of inter-cluster regions, we also would like</span></span>
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109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to have the coordinates of all aligned clusters on the fwd strand</span></span>
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110
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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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111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">end_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_coord</span></span>
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112
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">start_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_coord</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span></span>
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113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">end_coord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start_coord</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span></span>
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115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">fname_to_contigid_to_coords</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">][</span><span class="n" style="color: #333;">contig_id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">start_coord</span><span class="p">,</span> <span class="n" style="color: #333;">end_coord</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_idx</span><span class="p">))</span></span>
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116
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117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Write remaining sequences</span></span>
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118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" 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;">curr_cluster_seqs</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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119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" 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;">output_maf_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">maf_out</span><span class="p">:</span></span>
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120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MafWriter</span><span class="p">(</span><span class="n" style="color: #333;">maf_out</span><span class="p">)</span></span>
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121
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">msa_record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MultipleSeqAlignment</span><span class="p">(</span><span class="n" style="color: #333;">curr_cluster_seqs</span><span class="p">)</span></span>
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122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">msa_record</span><span class="p">.</span><span class="n" style="color: #333;">_annotations</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"pass"</span><span class="p">:</span> <span class="n" style="color: #333;">curr_cluster_idx</span><span class="p">}</span></span>
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123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write_alignment</span><span class="p">(</span><span class="n" style="color: #333;">msa_record</span><span class="p">)</span></span>
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124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fname_to_contigid_to_coords</span></span>
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125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#%%</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_intercluster_regions</span><span class="p">(</span><span class="n" style="color: #333;">input_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_directory</span><span class="p">,</span> <span class="n" style="color: #333;">fname_to_contigid_to_coords</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_to_adjacent_clusters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" 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;">glob</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_directory</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/*.fa*"</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC131" 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="n" style="color: #333;">f</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fasta_f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">input_sequences</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC133" 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;">fasta_f</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">fasta_f</span><span class="p">).</span><span class="n" style="color: #333;">name</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC135" 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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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"+"</span><span class="p">,</span> <span class="s" style="color: #d14;">"START CAP"</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">fname_to_contigid_to_coords</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">][</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">),</span> <span class="s" style="color: #d14;">"+"</span><span class="p">,</span> <span class="s" style="color: #d14;">"END CAP"</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_idx</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">prev_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">next_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">fwd</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"right"</span><span class="p">,</span> <span class="s" style="color: #d14;">"left"</span></span>
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142
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC142" 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;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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143
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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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144
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">fwd</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev</span><span class="p">,</span> <span class="n" style="color: #333;">fwd</span></span>
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146
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq = seq.reverse_complement()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)][(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">prev_end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)][(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">fwd</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">next_start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)][(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="s" style="color: #d14;">"right"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</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="s" style="color: #d14;">"left"</span><span class="p">)</span></span>
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150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)][(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">fwd</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="s" style="color: #d14;">"left"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</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="s" style="color: #d14;">"right"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_to_adjacent_clusters</span><span class="p">[(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">fwd</span><span class="p">)].</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="s" style="color: #d14;">"left"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</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="s" style="color: #d14;">"right"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_to_adjacent_clusters</span><span class="p">[(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span><span class="p">)].</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="s" style="color: #d14;">"right"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</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="s" style="color: #d14;">"left"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">seq_to_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">prev_end</span><span class="p">:</span><span class="n" style="color: #333;">start</span><span class="p">].</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">:<-file:contig->:</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">description</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="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" 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="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_directory</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/cluster</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_idx</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">rev</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">([</span><span class="n" style="color: #333;">seq_to_write</span><span class="p">],</span> <span class="n" style="color: #333;">out_f</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">seq_to_write</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">:</span><span class="n" style="color: #333;">next_start</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">:<-file:contig->:</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">description</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="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" 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="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_directory</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/cluster</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_idx</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fwd</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">([</span><span class="n" style="color: #333;">seq_to_write</span><span class="p">],</span> <span class="n" style="color: #333;">out_f</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span></span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#%%</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_new_extensions</span><span class="p">(</span><span class="n" style="color: #333;">cluster_files</span><span class="p">,</span> <span class="n" style="color: #333;">match_score</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch_score</span><span class="p">,</span> <span class="n" style="color: #333;">gap_penalty</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># mat = substitution_matrices.load("NUC.4.4")</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># mismatch_multiplier = 1</span></span>
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164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># gap_match = -1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">fname_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"^.*/cluster(\d+)-(.*).fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">))</span></span>
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167
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_expand</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cluster_f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cluster_files</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_parser</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">cluster_f</span><span class="p">).</span><span class="n" style="color: #333;">groups</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">cluster_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">sequences</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;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">cluster_f</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sequences</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">score_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_len</span><span class="p">[(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Counter</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">].</span><span class="n" style="color: #333;">upper</span><span class="p">()</span> <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;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">idx</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"-"</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sequences</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n1</span><span class="p">,</span> <span class="n" style="color: #333;">n2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">combinations</span><span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">r</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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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">n2</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="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gap_penalty</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="n" style="color: #333;">n1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="n" style="color: #333;">n2</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC182" 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="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mismatch_score</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="n" style="color: #333;">n1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="n" style="color: #333;">n2</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nuc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bases</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nuc</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="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC187" 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="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">match_score</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="n" style="color: #333;">nuc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="n" style="color: #333;">nuc</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">score_list</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">score_list</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">score</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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191
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">extend_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">argmax</span><span class="p">(</span><span class="n" style="color: #333;">score_list</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># extend_by = lengths.most_common()[0][0] if len(lengths) == 1 else (lengths.most_common()[0][0] if lengths.most_common()[0][0] != 0 else lengths.most_common()[1][0])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print(lengths)</span></span>
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195
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># extend_by = min(extend_by, 100)</span></span>
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196
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_expand</span><span class="p">[(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extend_by</span></span>
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197
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">clusterdir_expand</span><span class="p">,</span> <span class="n" style="color: #333;">clusterdir_len</span></span>
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198
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199
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#%%</span></span>
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200
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201
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC201" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_xmfa_header</span><span class="p">(</span><span class="n" style="color: #333;">extended_xmfa_file</span><span class="p">,</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">,</span> <span class="n" style="color: #333;">num_clusters</span><span class="p">):</span></span>
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202
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203
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" 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;">extended_xmfa_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">xmfa_out</span><span class="p">:</span></span>
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204
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### Write header</span></span>
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205
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#FormatVersion Parsnp v1.1</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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206
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"#SequenceCount </span><span class="si" style="color: #d14;">{</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">)</span><span class="si" 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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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">),</span> <span class="n" style="color: #333;">global_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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208
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"##SequenceIndex </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">global_idx</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="si" 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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209
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"##SequenceFile </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname</span><span class="si" 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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210
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"##SequenceHeader ></span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">header</span><span class="si" 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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211
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"##SequenceLength </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">)]</span><span class="si" 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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212
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"##IntervalCount </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">num_clusters</span><span class="si" 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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213
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214
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_xmfa_cluster</span><span class="p">(</span><span class="n" style="color: #333;">extended_xmfa_file</span><span class="p">,</span> <span class="n" style="color: #333;">msa_records</span><span class="p">,</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">):</span></span>
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216
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC216" 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;">extended_xmfa_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">xmfa_out</span><span class="p">:</span></span>
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217
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### Write MSA record</span></span>
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218
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">header_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"(.+):<-file:contig->:(.+)"</span><span class="p">)</span></span>
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219
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">msa_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">msa_records</span><span class="p">:</span></span>
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220
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">'cluster'</span><span class="p">]</span></span>
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221
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">msa_record</span><span class="p">:</span></span>
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222
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_parser</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">).</span><span class="n" style="color: #333;">groups</span><span class="p">()</span></span>
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223
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224
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"+"</span></span>
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225
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">]</span></span>
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226
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"size"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
227
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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="new_line diff-line-num new" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">:</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">start</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">size</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
229
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC229" 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="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
230
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">:</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">size</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">start</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
231
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">strand</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> cluster</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> s1:p</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">start</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
232
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">msa_record</span><span class="p">,</span> <span class="n" style="color: #333;">xmfa_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC237" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># fname_to_contigid_to_extended = defaultdict(lambda: defaultdict(list))</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC238" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># fname_to_contigid_to_coords[fname][contig_id].append((seqrecord.annotations["start"], seqrecord.annotations["start"] + seqrecord.annotations["size"], strand, cluster_idx))</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC239" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_extended_xmfa</span><span class="p">(</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">header_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"(.+):<-file:contig->:(.+)"</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">clusters</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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251
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contigid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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252
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cluster</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contigid</span><span class="p">)].</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">clusters</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">cluster</span><span class="p">)</span></span>
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254
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">write_xmfa_header</span><span class="p">(</span><span class="n" style="color: #333;">extended_maf_file</span><span class="p">,</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">,</span> <span class="n" style="color: #333;">cluster</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC255" 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;">original_maf_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">maf_in</span><span class="p">:</span></span>
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256
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">maf_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MafIterator</span><span class="p">(</span><span class="n" style="color: #333;">maf_in</span><span class="p">)</span></span>
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257
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># maf_writer = MafWriter(maf_out)</span></span>
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258
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># maf_writer = MauveWriter(maf_out)</span></span>
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259
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># maf_writer.write_header()</span></span>
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260
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="n" style="color: #333;">msa_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">maf_iterator</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_parser</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">msa_record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nb" style="color: #0086b3;">id</span><span class="p">).</span><span class="n" style="color: #333;">groups</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">cluster_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">msa_record</span><span class="p">.</span><span class="n" style="color: #333;">_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"pass"</span><span class="p">])</span></span>
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263
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">direction</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"right"</span><span class="p">,</span> <span class="s" style="color: #d14;">"left"</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">expand_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clusterdir_expand</span><span class="p">[(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)]</span></span>
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265
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">expand_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span></span>
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266
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">expand_by</span><span class="p">,</span> </span>
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267
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">cldir_to_len</span><span class="p">[(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cldir_to_len</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>
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268
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="p">)</span> </span>
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269
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># expand_by = min(expand_by, 7)</span></span>
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270
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># expand_by = 10</span></span>
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271
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for seq_record in msa_record:</span></span>
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272
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fname, contig_id, cluster_idx = header_parser.match(seq_record.id).groups()</span></span>
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273
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># cluster_idx = int(cluster_idx)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># expand_by = min(expand_by, fname_contigid_to_cluster_dir_to_length[(fname, contig_id)][(cluster_idx, direction)])</span></span>
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275
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">expand_by</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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276
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC277" 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="sa">f</span><span class="s" style="color: #d14;">"Expanding cluster </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_idx</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> to the </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">direction</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> by </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">expand_by</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">inter_cluster_sequences</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;">index</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_directory</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/cluster</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cluster_idx</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">-</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">direction</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">msa_record</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_parser</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">).</span><span class="n" style="color: #333;">groups</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">cluster_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">flanking_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inter_cluster_sequences</span><span class="p">[</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">fname</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">:<-file:contig->:</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">contig_id</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">flanking_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">[:</span><span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">)][(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)]]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC284" 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;">flanking_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">expand_by</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">[:</span><span class="n" style="color: #333;">expand_by</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"left"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">expand_by</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">flanking_seq</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" 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="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"-"</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">expand_by</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">flanking_seq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"size"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</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="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"right"</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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294
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span></span>
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296
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="p">(</span><span class="n" style="color: #333;">expand_by</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">adj_cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">adj_cluster_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">)][(</span><span class="n" style="color: #333;">cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">)][(</span><span class="n" style="color: #333;">adj_cluster_idx</span><span class="p">,</span> <span class="n" style="color: #333;">adj_cluster_dir</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">-=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">flanking_seq</span><span class="p">.</span><span class="n" style="color: #333;">seq</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="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>
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299
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300
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301
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302
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for seq_record in msa_record:</span></span>
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303
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fname, contig_id = header_parser.match(seq_record.id).groups()</span></span>
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304
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq_record.id = contig_id</span></span>
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305
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">msa_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"cluster"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_idx</span></span>
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306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">write_xmfa_cluster</span><span class="p">(</span><span class="n" style="color: #333;">extended_maf_file</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">msa_record</span><span class="p">],</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">)</span></span>
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307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># maf_writer.write_alignment(msa_record)</span></span>
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308
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309
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC309" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#%%</span></span>
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310
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC310" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_maf</span><span class="p">(</span><span class="n" style="color: #333;">maf_file</span><span class="p">,</span> <span class="n" style="color: #333;">fname_to_seqrecords</span><span class="p">):</span></span>
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311
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">contig_to_coords_test</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>
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312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">header_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">"(.+):<-file:contig->:(.+)"</span><span class="p">)</span></span>
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313
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC313" 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;">maf_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">maf_in</span><span class="p">:</span></span>
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314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">maf_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MafIterator</span><span class="p">(</span><span class="n" style="color: #333;">maf_in</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">msa_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">maf_iterator</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">msa_record</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">coord_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"srcSize"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]</span></span>
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320
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"size"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">coord_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coord_start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"size"</span><span class="p">]</span></span>
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323
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">coord_start</span><span class="p">,</span> <span class="n" style="color: #333;">coord_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coord_end</span><span class="p">,</span> <span class="n" style="color: #333;">coord_start</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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325
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">coord_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
326
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header_parser</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">).</span><span class="n" style="color: #333;">groups</span><span class="p">()</span></span>
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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
327
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">contig_to_coords_test</span><span class="p">[(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">contig_id</span><span class="p">)].</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">coord_start</span><span class="p">,</span> <span class="n" style="color: #333;">coord_end</span><span class="p">,</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"strand"</span><span class="p">]))</span></span>
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328
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if len(seq_record) > 20:</span></span>
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329
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print(seq_record.id.split(":")[0], seq[:15],"...", seq[-15:])</span></span>
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330
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># else:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
331
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print(seq_record.id.split(":")[0], seq)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
332
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">block_seq</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;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">lower</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="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"n"</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">)</span></span>
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333
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">original_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname_to_seqrecords</span><span class="p">[</span><span class="n" style="color: #333;">fname</span><span class="p">][</span><span class="n" style="color: #333;">contig_id</span><span class="p">].</span><span class="n" style="color: #333;">seq</span></span>
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<td class="new_line diff-line-num new" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
334
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
335
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">match_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">block_seq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">original_seq</span><span class="p">),</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">IGNORECASE</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
336
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC336" 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="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
337
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">original_seq</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;">original_seq</span><span class="p">.</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">())</span></span>
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">match_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">block_seq</span><span class="p">,</span> <span class="n" style="color: #333;">original_seq</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">IGNORECASE</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">match_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match_pos</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match_pos</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">match_pos</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="s" style="color: #d14;">"!="</span><span class="p">,</span> <span class="n" style="color: #333;">match_pos</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
342
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
343
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">block_seq</span><span class="p">)</span></span>
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345
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
346
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_to_coords_test</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
347
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">contig_to_coords_test</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">contig_to_coords_test</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
348
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">contig_to_coords_test</span></span>
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349
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC349" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
350
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC350" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate_coords</span><span class="p">(</span><span class="n" style="color: #333;">contig_to_coords</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_to_coords</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
352
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">prev_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
353
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span><span class="p">:</span></span>
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354
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">prev_end</span><span class="p">:</span></span>
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355
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">contig</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> has invalid coordinates!"</span><span class="p">)</span></span>
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356
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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357
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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358
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">prev_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span></span>
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359
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC359" class="line" lang="python"></span>
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360
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC360" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># coords_extended = check_maf("parsnp-extended.maf")</span></span>
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361
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC361" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># validate_coords(coords_extended)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
362
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC362" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># coords_original = check_maf("parsnp.maf")</span></span>
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363
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC363" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#%%</span></span>
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364
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC364" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># validate = True</span></span>
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365
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC365" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># genome_dir = "sars-100-rev/"</span></span>
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366
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC366" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># sequence_files = glob(f"{genome_dir}/*.fa*")</span></span>
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367
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC367" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># xmfa_file = f"{genome_dir}/parsnp.xmfa"</span></span>
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368
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC368" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># original_maf_file = f"{genome_dir}/parsnp-original.maf"</span></span>
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369
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC369" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># extended_maf_file = f"{genome_dir}/parsnp-extended.maf"</span></span>
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370
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC370" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># cluster_directory = "clusters/"</span></span>
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371
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC371" class="line" lang="python"></span>
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC372" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># fname_contigid_to_length, fname_contigidx_to_header, fname_to_seqrecord = get_sequence_data(sequence_files, index_files=validate)</span></span>
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373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC373" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># fname_to_contigid_to_coords = xmfa_to_maf(xmfa_file, original_maf_file, fname_contigidx_to_header, fname_contigid_to_length)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC374" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># packed_write_result = write_intercluster_regions(cluster_directory, fname_to_contigid_to_coords)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC375" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># fname_contigid_to_cluster_dir_to_length, fname_contigid_to_cluster_dir_to_adjacent_cluster = packed_write_result</span></span>
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376
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC376" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># cluster_files = glob(f"{cluster_directory}/*.fasta")</span></span>
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377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC377" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># clusterdir_expand, clusterdir_len = get_new_extensions(cluster_files)</span></span>
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378
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC378" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># write_extended_maf(</span></span>
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379
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># original_maf_file,</span></span>
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380
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># extended_maf_file,</span></span>
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381
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># cluster_directory,</span></span>
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382
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clusterdir_expand,</span></span>
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383
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clusterdir_len,</span></span>
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384
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fname_contigid_to_cluster_dir_to_length,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fname_contigid_to_cluster_dir_to_adjacent_cluster)</span></span>
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386
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC386" class="line" lang="python"></span>
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387
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC387" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># if validate:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># coords_extended = check_maf(extended_maf_file, fname_to_seqrecord)</span></span>
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389
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># validate_coords(coords_extended)</span></span>
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390
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># coords_original = check_maf(original_maf_file, fname_to_seqrecord)</span></span>
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391
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># validate_coords(coords_original)</span></span></pre></td>
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<li id="ea7cb5eaec19ba9bd46df58c8e1a23cc5da4247c">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#ea7cb5eaec19ba9bd46df58c8e1a23cc5da4247c"><strong>logger.py</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">############################################# Logging ##############################################</span></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">BLACK</span><span class="p">,</span> <span class="n" style="color: #333;">RED</span><span class="p">,</span> <span class="n" style="color: #333;">GREEN</span><span class="p">,</span> <span class="n" style="color: #333;">YELLOW</span><span class="p">,</span> <span class="n" style="color: #333;">BLUE</span><span class="p">,</span> <span class="n" style="color: #333;">MAGENTA</span><span class="p">,</span> <span class="n" style="color: #333;">CYAN</span><span class="p">,</span> <span class="n" style="color: #333;">WHITE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#These are the sequences need to get colored ouput</span></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">CSI</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#"\x1B["</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">BOLDME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[1m'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">STATUS_BLUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[94m'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">OK_GREEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[92m'#'32m'</span></span>
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9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">SKIP_GRAY</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[37m'</span></span>
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">WARNING_YELLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[93m'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">ERROR_RED</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[91m'</span></span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">ENDC</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'0m'</span></span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">RESET_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[0m"</span></span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">COLOR_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[1;%dm"</span></span>
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">BOLD_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[1m"</span></span>
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16
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">formatter_message</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">use_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_color</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$RESET"</span><span class="p">,</span> <span class="n" style="color: #333;">RESET_SEQ</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$BOLD"</span><span class="p">,</span> <span class="n" style="color: #333;">BOLD_SEQ</span><span class="p">)</span></span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$RESET"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$BOLD"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">message</span></span>
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23
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">COLORS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'DEBUG'</span><span class="p">:</span> <span class="n" style="color: #333;">BLUE</span><span class="p">,</span></span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'INFO'</span><span class="p">:</span> <span class="n" style="color: #333;">WHITE</span><span class="p">,</span></span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'WARNING'</span><span class="p">:</span> <span class="n" style="color: #333;">YELLOW</span><span class="p">,</span></span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'ERROR'</span><span class="p">:</span> <span class="n" style="color: #333;">RED</span><span class="p">,</span></span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'CRITICAL'</span><span class="p">:</span> <span class="n" style="color: #333;">RED</span></span>
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30
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31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ColoredFormatter</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">):</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">datefmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">use_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">datefmt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">datefmt</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">use_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">use_color</span></span>
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37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">levelname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">levelname</span></span>
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39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">use_color</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">levelname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">COLORS</span><span class="p">:</span></span>
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40
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">levelname_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">COLOR_SEQ</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">30</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COLORS</span><span class="p">[</span><span class="n" style="color: #333;">levelname</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">levelname</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">RESET_SEQ</span></span>
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41
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">levelname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">levelname_color</span></span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Instantiate logger</span></span>
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45
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="s" style="color: #d14;">"Parsnp"</span><span class="p">)</span></span>
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46
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">()</span></span>
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48
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># create formatter and add it to the handlers</span></span>
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50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">formatter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ColoredFormatter</span><span class="p">(</span><span class="s" style="color: #d14;">'%(asctime)s - %(levelname)s - %(message)s'</span><span class="p">,</span></span>
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51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">datefmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"%H:%M:%S"</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="n" style="color: #333;">formatter</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add the handlers to the logger</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">####################################################################################################</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#3849e3531855982fc7f5e63b3b17488714940ae3"><strong>parsnp</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># See the LICENSE file included with this software for license information.</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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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="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">getopt</span><span class="p">,</span> <span class="n" style="color: #333;">random</span><span class="p">,</span><span class="n" style="color: #333;">subprocess</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="p">,</span><span class="idiff left deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">glob</span></span><span class="p"><span class="idiff right deletion">,</span></span><span class="n" style="color: #333;">operator</span><span class="p">,</span> <span class="n" style="color: #333;">math</span><span class="p">,</span> <span class="n" style="color: #333;">datetime</span><span class="p">,</span><span class="n" style="color: #333;">numpy</span> <span class="c1" style="color: #998; font-style: italic;">#pysam</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">getopt</span><span class="p">,</span> <span class="n" style="color: #333;">random</span><span class="p">,</span><span class="n" style="color: #333;">subprocess</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="p">,</span><span class="n" style="color: #333;">operator</span><span class="p">,</span> <span class="n" style="color: #333;">math</span><span class="p">,</span> <span class="n" style="color: #333;">datetime</span><span class="p">,</span><span class="n" style="color: #333;">numpy</span> <span class="c1" style="color: #998; font-style: italic;">#pysam</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">csv</span></span>
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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="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">tempfile</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tempfile</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TemporaryDirectory</span></span>
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">logger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">logger</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">signal</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" 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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16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">glob</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">glob</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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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="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;">"1.6.2"</span></span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">extend</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ext</span></span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" 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;">"1.7.2"</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" 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">@@ -37,60 +42,6 @@ TOTSEQS=0</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">PARSNP_DIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>
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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="LC40" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">############################################# Logging ##############################################</span></span>
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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="LC41" class="line" lang="python"><span class="n" style="color: #333;">BLACK</span><span class="p">,</span> <span class="n" style="color: #333;">RED</span><span class="p">,</span> <span class="n" style="color: #333;">GREEN</span><span class="p">,</span> <span class="n" style="color: #333;">YELLOW</span><span class="p">,</span> <span class="n" style="color: #333;">BLUE</span><span class="p">,</span> <span class="n" style="color: #333;">MAGENTA</span><span class="p">,</span> <span class="n" style="color: #333;">CYAN</span><span class="p">,</span> <span class="n" style="color: #333;">WHITE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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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="LC42" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#These are the sequences need to get colored ouput</span></span>
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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="LC43" class="line" lang="python"><span class="n" style="color: #333;">CSI</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#"\x1B["</span></span>
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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="LC44" class="line" lang="python"><span class="n" style="color: #333;">BOLDME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[1m'</span></span>
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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="LC45" class="line" lang="python"><span class="n" style="color: #333;">STATUS_BLUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[94m'</span></span>
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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="LC46" class="line" lang="python"><span class="n" style="color: #333;">OK_GREEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[92m'#'32m'</span></span>
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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="LC47" class="line" lang="python"><span class="n" style="color: #333;">SKIP_GRAY</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[37m'</span></span>
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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="LC48" class="line" lang="python"><span class="n" style="color: #333;">WARNING_YELLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[93m'</span></span>
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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="LC49" class="line" lang="python"><span class="n" style="color: #333;">ERROR_RED</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'\033[91m'</span></span>
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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="LC50" class="line" lang="python"><span class="n" style="color: #333;">ENDC</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="c1" style="color: #998; font-style: italic;">#CSI+'0m'</span></span>
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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="LC51" class="line" lang="python"><span class="n" style="color: #333;">RESET_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[0m"</span></span>
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52
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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="LC52" class="line" lang="python"><span class="n" style="color: #333;">COLOR_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[1;%dm"</span></span>
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53
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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">BOLD_SEQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[1m"</span></span>
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54
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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="LC54" class="line" lang="python"></span>
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55
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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="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">formatter_message</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">use_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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56
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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="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_color</span><span class="p">:</span></span>
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57
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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$RESET"</span><span class="p">,</span> <span class="n" style="color: #333;">RESET_SEQ</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$BOLD"</span><span class="p">,</span> <span class="n" style="color: #333;">BOLD_SEQ</span><span class="p">)</span></span>
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58
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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="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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59
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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$RESET"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"$BOLD"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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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="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">message</span></span>
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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="LC62" class="line" lang="python"><span class="n" style="color: #333;">COLORS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">'DEBUG'</span><span class="p">:</span> <span class="n" style="color: #333;">BLUE</span><span class="p">,</span></span>
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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="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">'INFO'</span><span class="p">:</span> <span class="n" style="color: #333;">WHITE</span><span class="p">,</span></span>
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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'WARNING'</span><span class="p">:</span> <span class="n" style="color: #333;">YELLOW</span><span class="p">,</span></span>
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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="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">'ERROR'</span><span class="p">:</span> <span class="n" style="color: #333;">RED</span><span class="p">,</span></span>
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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="LC67" class="line" lang="python"> <span class="s" style="color: #d14;">'CRITICAL'</span><span class="p">:</span> <span class="n" style="color: #333;">RED</span></span>
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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="LC68" class="line" lang="python"><span class="p">}</span></span>
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69
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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="LC69" class="line" lang="python"></span>
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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="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ColoredFormatter</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">):</span></span>
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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="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">datefmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">use_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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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="LC72" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">msg</span><span class="p">,</span> <span class="n" style="color: #333;">datefmt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">datefmt</span><span class="p">)</span></span>
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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="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">use_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">use_color</span></span>
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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="LC74" class="line" lang="python"></span>
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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="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>
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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="LC76" class="line" lang="python"> <span class="n" style="color: #333;">levelname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">levelname</span></span>
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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="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">use_color</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">levelname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">COLORS</span><span class="p">:</span></span>
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78
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<td class="new_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">levelname_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">COLOR_SEQ</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">30</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COLORS</span><span class="p">[</span><span class="n" style="color: #333;">levelname</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">levelname</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">RESET_SEQ</span></span>
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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="LC79" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">levelname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">levelname_color</span></span>
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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="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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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="LC81" class="line" lang="python"></span>
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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="LC82" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Instantiate logger</span></span>
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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="LC83" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="s" style="color: #d14;">"Parsnp"</span><span class="p">)</span></span>
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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="LC84" class="line" lang="python"><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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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="LC85" class="line" lang="python"><span class="n" style="color: #333;">ch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">()</span></span>
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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="LC86" class="line" lang="python"><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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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="LC87" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># create formatter and add it to the handlers</span></span>
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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="LC88" class="line" lang="python"><span class="n" style="color: #333;">formatter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ColoredFormatter</span><span class="p">(</span><span class="s" style="color: #d14;">'%(asctime)s - %(levelname)s - %(message)s'</span><span class="p">,</span></span>
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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="LC89" class="line" lang="python"> <span class="n" style="color: #333;">datefmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"%H:%M:%S"</span><span class="p">)</span></span>
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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="LC90" class="line" lang="python"><span class="n" style="color: #333;">ch</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="n" style="color: #333;">formatter</span><span class="p">)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add the handlers to the logger</span></span>
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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="LC92" class="line" lang="python"><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">ch</span><span class="p">)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">####################################################################################################</span></span>
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45
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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46
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">########################################### Environment ############################################</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="247" style="width: 35px; color: rgba(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">@@ -296,7 +247,7 @@ def is_valid_file_path(parser, arg):</td>
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296
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247
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC247" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_valid_dir</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">):</span></span>
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297
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248
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC248" 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;">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="n" style="color: #333;">arg</span><span class="p">):</span></span>
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298
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249
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span> <span class="s" style="color: #d14;">"The directory %s does not exist</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;">arg</span><span class="p">))</span></span>
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299
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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="LC299" 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;">glob</span><span class="p"><span class="idiff left deletion">.</span></span><span class="n" style="color: #333;"><span class="idiff right deletion">glob</span></span><span class="p">(</span><span class="s" style="color: #d14;">"%s/*"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">arg</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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250
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC250" 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;">glob</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/*"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">arg</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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300
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251
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"The director %s is empty"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">))</span></span>
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301
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252
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC252" class="line" lang="python"></span>
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302
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253
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></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">@@ -469,6 +420,26 @@ def parse_args():</td>
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469
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420
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "--filter-phipack-snps",</span></span>
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470
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421
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># action = "store_true",</span></span>
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422
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC422" 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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423
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">extend_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;">"LCB Extension"</span><span class="p">)</span></span>
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424
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">extend_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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425
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="s" style="color: #d14;">"--extend-lcbs"</span><span class="p">,</span></span>
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426
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC426" 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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427
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC427" 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;">"Extend the boundaries of LCBs with an ungapped alignment"</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">extend_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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429
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="s" style="color: #d14;">"--match-score"</span><span class="p">,</span></span>
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430
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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431
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">,</span></span>
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432
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC432" 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;">"Value of match score for extension"</span><span class="p">)</span></span>
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433
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">extend_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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434
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC434" class="line" lang="python"> <span class="s" style="color: #d14;">"--mismatch-penalty"</span><span class="p">,</span></span>
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435
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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436
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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437
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC437" 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;">"Value of mismatch score for extension (should be negative)"</span><span class="p">)</span></span>
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438
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">extend_args</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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439
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="s" style="color: #d14;">"--gap-penalty"</span><span class="p">,</span></span>
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440
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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441
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">default</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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442
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC442" 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;">"Value of gap penalty for extension (should be negative)"</span><span class="p">)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC443" class="line" lang="python"></span>
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444
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC444" 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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445
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC445" 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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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -540,8 +511,7 @@ def parse_args():</td>
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511
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC511" class="line" lang="python"></span>
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512
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC512" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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513
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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543
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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="LC543" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="n" style="color: #333;">BOLDME</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"|--Parsnp %s--|</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;">VERSION</span><span class="p">))</span></span>
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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="LC544" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="n" style="color: #333;">BOLDME</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"For detailed documentation please see --> http://harvest.readthedocs.org/en/latest</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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514
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC514" 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="sa">f</span><span class="s" style="color: #d14;">"|--Parsnp </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">VERSION</span><span class="si" style="color: #d14;">}</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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515
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC515" class="line" lang="python"></span>
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516
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC516" class="line" lang="python"></span>
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547
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517
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">parsnp_dir</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">0</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">@@ -650,17 +620,18 @@ if __name__ == "__main__":</td>
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650
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620
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC620" 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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651
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621
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC621" 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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622
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC622" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><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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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><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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656
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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="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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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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662
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<td class="new_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(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="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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><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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623
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC623" 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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<td class="new_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
624
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
625
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">records</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;">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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<td class="new_line diff-line-num new" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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627
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC627" 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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<td class="new_line diff-line-num new" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC628" 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;">extend_lcbs</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;">records</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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<td class="new_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
629
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC629" 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;">"Extending LCBs does not currently work with multi-contig inputs yet"</span><span class="p">)</span></span>
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630
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC630" 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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<td class="new_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
631
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC631" 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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<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
632
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC632" 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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633
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC633" 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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634
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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664
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635
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC635" class="line" lang="python"></span>
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636
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Parse reference if necessary</span></span>
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666
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637
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC637" 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="884" style="width: 35px; color: rgba(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="855" style="width: 35px; color: rgba(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">@@ -884,28 +855,34 @@ SETTINGS:</td>
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884
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855
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC855" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># fnafiles.remove(ref)</span></span>
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885
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856
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC856" class="line" lang="python"></span>
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886
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857
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC857" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#sort reference by largest replicon to smallest</span></span>
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887
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC887" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sortem</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">autopick_ref</span><span class="p">:</span></span>
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888
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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="LC888" 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;">"Sorting reference replicons"</span><span class="p">)</span></span>
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889
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC889" class="line" lang="python"> <span class="n" style="color: #333;">ff</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;">ref</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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890
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC890" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ff</span><span class="p">.</span><span class="n" style="color: #333;">read</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>
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891
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC891" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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892
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC892" class="line" lang="python"> <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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893
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC893" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqs</span><span class="p">:</span></span>
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894
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC894" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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895
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC895" class="line" lang="python"> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <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 class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
896
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC896" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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897
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC897" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO Why do we ignore when theres a header but no sequence?</span></span>
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898
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC898" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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899
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC899" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span><span class="p">[</span><span class="n" style="color: #333;">hdr</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span></span>
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900
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC900" class="line" lang="python"> <span class="n" style="color: #333;">seq_len</span><span class="p">[</span><span class="n" style="color: #333;">hdr</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</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="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">count</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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901
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC901" class="line" lang="python"> <span class="n" style="color: #333;">seq_len_sort</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">seq_len</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">operator</span><span class="p">.</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
902
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC902" class="line" lang="python"> <span class="n" style="color: #333;">ref</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="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;">basename</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".ref"</span><span class="p">)</span></span>
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903
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC903" class="line" lang="python"> <span class="n" style="color: #333;">ffo</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;">ref</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
904
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC904" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_len_sort</span><span class="p">:</span></span>
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905
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC905" class="line" lang="python"> <span class="n" style="color: #333;">ffo</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">%s</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;">hdr</span><span class="p">))</span></span>
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906
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC906" class="line" lang="python"> <span class="n" style="color: #333;">ffo</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">seq_dict</span><span class="p">[</span><span class="n" style="color: #333;">hdr</span><span class="p">]))</span></span>
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907
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<td class="new_line diff-line-num old" data-linenumber="858" style="width: 35px; color: rgba(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="LC907" class="line" lang="python"> <span class="n" style="color: #333;">ff</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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908
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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="LC908" class="line" lang="python"> <span class="n" style="color: #333;">ffo</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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858
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC858" 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;">in</span> <span class="n" style="color: #333;">fnafiles</span><span class="p">:</span></span>
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859
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">fnafiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">f</span> <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;">fnafiles</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ref</span><span class="p">]</span></span>
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860
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">sortem</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">autopick_ref</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
861
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">sequences</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;">ref</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
862
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">new_ref</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="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;">basename</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".ref"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
863
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">sequences</span><span class="p">,</span> <span class="n" style="color: #333;">new_ref</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
864
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_ref</span></span>
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865
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC865" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># logger.debug("Sorting reference replicons")</span></span>
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866
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC866" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ff = open(ref, 'r')</span></span>
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867
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seqs = ff.read().split(">")[1:]</span></span>
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868
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC868" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq_dict = {}</span></span>
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869
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC869" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq_len = {}</span></span>
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870
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC870" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for seq in seqs:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
871
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC871" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># try:</span></span>
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872
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC872" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># hdr, seq = seq.split("\n",1)</span></span>
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873
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC873" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># except ValueError:</span></span>
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874
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC874" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # TODO Why do we ignore when theres a header but no sequence?</span></span>
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875
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC875" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># continue</span></span>
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876
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC876" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq_dict[hdr] = seq</span></span>
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<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
877
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC877" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq_len[hdr] = len(seq) - seq.count('\n')</span></span>
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<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
878
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC878" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># seq_len_sort = sorted(iter(seq_len.items()), key=operator.itemgetter(1), reverse=True)</span></span>
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879
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC879" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ref = os.path.join(outputDir, os.path.basename(ref)+".ref")</span></span>
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880
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC880" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ffo = open(ref, 'w')</span></span>
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881
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC881" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for hdr, seq in seq_len_sort:</span></span>
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882
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC882" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ffo.write(">%s\n"%(hdr))</span></span>
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883
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC883" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ffo.write("%s"%(seq_dict[hdr]))</span></span>
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884
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC884" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ff.close()</span></span>
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885
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC885" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ffo.close()</span></span>
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909
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886
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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910
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887
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC887" class="line" lang="python"> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genbank_ref</span></span>
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911
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888
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC888" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="948" style="width: 35px; color: rgba(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="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -948,7 +925,7 @@ SETTINGS:</td>
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948
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925
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC925" 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="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;">"alltogether.fasta"</span><span class="p">)):</span></span>
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949
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926
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC926" 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="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;">"alltogether.fasta"</span><span class="p">))</span></span>
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950
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927
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC927" 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="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;">"blocks/b1"</span><span class="p">)):</span></span>
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951
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<td class="new_line diff-line-num old" data-linenumber="928" style="width: 35px; color: rgba(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="LC951" class="line" lang="python"> <span class="n" style="color: #333;">ftrm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left deletion">glob</span></span><span class="p"><span class="idiff right deletion">.</span></span><span class="n" style="color: #333;">glob</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;">"blocks/b*"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC928" class="line" lang="python"> <span class="n" style="color: #333;">ftrm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</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;">"blocks/b*"</span><span class="p">))</span></span>
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952
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<td class="new_line diff-line-num" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
929
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC929" 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;">ftrm</span><span class="p">:</span></span>
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953
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930
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC930" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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954
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931
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC931" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1240" style="width: 35px; color: rgba(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="1217" style="width: 35px; color: rgba(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">@@ -1240,7 +1217,7 @@ Please verify recruited genomes are all strain of interest""")</td>
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1240
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1217
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1217" class="line" lang="python"> <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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1241
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<td class="new_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1218" class="line" lang="python"> <span class="n" style="color: #333;">elapsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">t2</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="n" style="color: #333;">t1</span><span class="p">)</span></span>
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1242
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1219
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1219" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("-->Getting list of LCBs.."</span></span>
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1243
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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="LC1243" class="line" lang="python"> <span class="n" style="color: #333;">allbfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left deletion">glob</span></span><span class="p"><span class="idiff right deletion">.</span></span><span class="n" style="color: #333;">glob</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;">blocks_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"b*/*"</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1220
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1220" class="line" lang="python"> <span class="n" style="color: #333;">allbfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</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;">blocks_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"b*/*"</span><span class="p">))</span></span>
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1244
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1221
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1221" class="line" lang="python"> <span class="n" style="color: #333;">blockfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1245
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1222
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1222" class="line" lang="python"> <span class="n" style="color: #333;">block_startpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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1246
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1223
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1223" class="line" lang="python"> <span class="n" style="color: #333;">block_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1357" style="width: 35px; color: rgba(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="1334" style="width: 35px; color: rgba(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">@@ -1357,7 +1334,7 @@ Please verify recruited genomes are all strain of interest""")</td>
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1357
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1334
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1334" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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1358
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<td class="new_line diff-line-num" data-linenumber="1335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1335
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1335" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">()</span></span>
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1359
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1336
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1336" class="line" lang="python"> <span class="n" style="color: #333;">brkeys</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;">bedfile_dict</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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1360
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<td class="new_line diff-line-num old" data-linenumber="1337" style="width: 35px; color: rgba(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="LC1360" class="line" lang="python"> <span class="n" style="color: #333;">brkeys</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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1337
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1337" class="line" lang="python"> <span class="n" style="color: #333;">brkeys</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span><span class="idiff left right addition"> </span></span>
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1361
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1338
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1338" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">brkeys</span><span class="p">:</span></span>
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1362
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1339
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1339" class="line" lang="python"> <span class="n" style="color: #333;">bedfile</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">bedfile_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">])</span></span>
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1363
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1340
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1340" class="line" lang="python"> <span class="n" style="color: #333;">bedfile</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1343" style="width: 35px; color: rgba(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">@@ -1366,15 +1343,52 @@ Please verify recruited genomes are all strain of interest""")</td>
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1366
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1343
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1343" class="line" lang="python"></span>
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1367
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1344
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1344" class="line" lang="python"> <span class="n" style="color: #333;">annotation_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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1368
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1345
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1345" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#TODO always using xtrafast?</span></span>
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1346
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1346" class="line" lang="python"> <span class="n" style="color: #333;">parsnp_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">outputDir</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/parsnp.xmfa"</span></span>
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1347
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1347" 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;">extend_lcbs</span><span class="p">:</span></span>
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1348
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1348" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">outputDir</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/parsnp.xmfa"</span></span>
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1349
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1349" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</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;">temp_directory</span><span class="p">:</span></span>
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1350
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1350" class="line" lang="python"> <span class="n" style="color: #333;">original_maf_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">temp_directory</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/parsnp-original.maf"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1351
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1351" class="line" lang="python"> <span class="n" style="color: #333;">extended_xmfa_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">outputDir</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/parsnp-extended.xmfa"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1352
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1352" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigidx_to_header</span><span class="p">,</span> <span class="n" style="color: #333;">fname_to_seqrecord</span><span class="p">,</span> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ext</span><span class="p">.</span><span class="n" style="color: #333;">get_sequence_data</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1353
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1353" class="line" lang="python"> <span class="n" style="color: #333;">ref</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1354
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1354" class="line" lang="python"> <span class="n" style="color: #333;">finalfiles</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1355
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1355" class="line" lang="python"> <span class="n" style="color: #333;">index_files</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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<td class="new_line diff-line-num new" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1356
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1356" class="line" lang="python"> <span class="n" style="color: #333;">fname_to_contigid_to_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ext</span><span class="p">.</span><span class="n" style="color: #333;">xmfa_to_maf</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1357
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1357" class="line" lang="python"> <span class="n" style="color: #333;">xmfa_file</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1358
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1358" class="line" lang="python"> <span class="n" style="color: #333;">original_maf_file</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1359
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1359" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigidx_to_header</span><span class="p">,</span> </span>
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1360
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1360" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1361
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1361" class="line" lang="python"> <span class="n" style="color: #333;">packed_write_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ext</span><span class="p">.</span><span class="n" style="color: #333;">write_intercluster_regions</span><span class="p">(</span><span class="n" style="color: #333;">finalfiles</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="n" style="color: #333;">temp_directory</span><span class="p">,</span> <span class="n" style="color: #333;">fname_to_contigid_to_coords</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1362
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1362" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">,</span> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">packed_write_result</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1363
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1363" class="line" lang="python"> <span class="n" style="color: #333;">cluster_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">temp_directory</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">/*.fasta"</span><span class="p">)</span></span>
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1364
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1364" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_expand</span><span class="p">,</span> <span class="n" style="color: #333;">clusterdir_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ext</span><span class="p">.</span><span class="n" style="color: #333;">get_new_extensions</span><span class="p">(</span></span>
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1365
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1365" class="line" lang="python"> <span class="n" style="color: #333;">cluster_files</span><span class="p">,</span></span>
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1366
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1366" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">match_score</span><span class="p">,</span></span>
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1367
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1367" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mismatch_penalty</span><span class="p">,</span></span>
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1368
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1368" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gap_penalty</span><span class="p">)</span></span>
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1369
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1369" class="line" lang="python"> <span class="n" style="color: #333;">ext</span><span class="p">.</span><span class="n" style="color: #333;">write_extended_xmfa</span><span class="p">(</span></span>
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1370
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1370" class="line" lang="python"> <span class="n" style="color: #333;">original_maf_file</span><span class="p">,</span></span>
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1371
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1371" class="line" lang="python"> <span class="n" style="color: #333;">extended_xmfa_file</span><span class="p">,</span></span>
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1372
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1372" class="line" lang="python"> <span class="n" style="color: #333;">temp_directory</span><span class="p">,</span></span>
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1373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1373" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_expand</span><span class="p">,</span></span>
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1374
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1374" class="line" lang="python"> <span class="n" style="color: #333;">clusterdir_len</span><span class="p">,</span></span>
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1375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1375" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_length</span><span class="p">,</span></span>
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1376
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1376" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_cluster_dir_to_adjacent_cluster</span><span class="p">,</span></span>
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1377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1377" class="line" lang="python"> <span class="n" style="color: #333;">fname_header_to_gcontigidx</span><span class="p">,</span></span>
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1378
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1378" class="line" lang="python"> <span class="n" style="color: #333;">fname_contigid_to_length</span><span class="p">)</span></span>
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1379
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1379" class="line" lang="python"> <span class="n" style="color: #333;">parsnp_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extended_xmfa_file</span></span>
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1380
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1380" 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="n" style="color: #333;">original_maf_file</span><span class="p">)</span></span>
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1381
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1381" class="line" lang="python"></span>
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1382
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1382" class="line" lang="python"></span>
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1369
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1383
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1383" 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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1370
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1384
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1384" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#add genbank here, if present</span></span>
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<td class="old_line diff-line-num" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1371
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1385
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1385" 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;">genbank_ref</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="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="1386" style="width: 35px; color: rgba(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="LC1372" class="line" lang="python"> <span class="n" style="color: #333;">rnc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"harvesttools -q -o <span class="idiff left deletion">%s</span>/parsnp.ggr -x <span class="idiff deletion">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">%</span></span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">outputDir</span></span><span class="p"><span class="idiff deletion">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">outputDir</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">os</span></span><span class="p"><span class="idiff deletion">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion">sep</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="s" style="color: #d14;"><span class="idiff right deletion">"parsnp.xmfa</span>"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1386
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1386" class="line" lang="python"> <span class="n" style="color: #333;">rnc</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa"><span class="idiff left addition">f</span></span><span class="s" style="color: #d14;">"harvesttools -q -o </span><span class="si" style="color: #d14;"><span class="idiff addition">{</span></span><span class="n" style="color: #333;"><span class="idiff addition">outputDir</span></span><span class="si" style="color: #d14;"><span class="idiff addition">}</span></span><span class="s" style="color: #d14;">/parsnp.ggr -x </span><span class="si" style="color: #d14;"><span class="idiff addition">{</span></span><span class="n" style="color: #333;"><span class="idiff addition">parsnp_output</span></span><span class="si" style="color: #d14;"><span class="idiff right addition">}</span></span><span class="s" style="color: #d14;">"</span></span>
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1373
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1387
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1387" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">genbank_files</span><span class="p">:</span></span>
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1374
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<td class="new_line diff-line-num" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1388
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1388" class="line" lang="python"> <span class="n" style="color: #333;">rnc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" -g %s "</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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1375
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<td class="new_line diff-line-num" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1389
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1389" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="n" style="color: #333;">rnc</span><span class="p">)</span></span>
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1376
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1390
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1390" 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 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="1391" style="width: 35px; color: rgba(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="LC1377" 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 -o <span class="idiff left deletion">%s</span>/parsnp.ggr -f <span class="idiff deletion">%s -x "</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">%</span></span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">outputDir</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="n" style="color: #333;"><span class="idiff deletion">ref</span></span><span class="p"><span class="idiff deletion">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">outputDir</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="n" style="color: #333;"><span class="idiff deletion">os</span></span><span class="p"><span class="idiff deletion">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion">sep</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="s" style="color: #d14;"><span class="idiff right deletion">"parsnp.xmfa</span>"</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1391" class="line" lang="python"> <span class="n" style="color: #333;">run_command</span><span class="p">(</span><span class="sa"><span class="idiff left addition">f</span></span><span class="s" style="color: #d14;">"harvesttools -q -o </span><span class="si" style="color: #d14;"><span class="idiff addition">{</span></span><span class="n" style="color: #333;"><span class="idiff addition">outputDir</span></span><span class="si" style="color: #d14;"><span class="idiff addition">}</span></span><span class="s" style="color: #d14;">/parsnp.ggr -f </span><span class="si" style="color: #d14;"><span class="idiff addition">{</span></span><span class="n" style="color: #333;"><span class="idiff addition">ref</span></span><span class="si" style="color: #d14;"><span class="idiff addition">}</span></span><span class="s" style="color: #d14;"><span class="idiff addition"> -x </span></span><span class="si" style="color: #d14;"><span class="idiff addition">{</span></span><span class="n" style="color: #333;"><span class="idiff addition">parsnp_output</span></span><span class="si" style="color: #d14;"><span class="idiff right addition">}</span></span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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1378
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<td class="new_line diff-line-num" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1392
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1392" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1379
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<td class="new_line diff-line-num" data-linenumber="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1393
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1393" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run_recomb_filter</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1380
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<td class="new_line diff-line-num" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1394
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1394" 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 -b %s/parsnp.rec,REC,</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">PhiPack</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> -o %s/parsnp.ggr -i %s/parsnp.ggr"</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="n" style="color: #333;">outputDir</span><span class="p">,</span><span class="n" style="color: #333;">outputDir</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1401" style="width: 35px; color: rgba(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">@@ -1387,14 +1401,14 @@ Please verify recruited genomes are all strain of interest""")</td>
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<td class="old_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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<td class="new_line diff-line-num" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1401
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1401" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1388
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<td class="new_line diff-line-num" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1402
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1402" 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="old_line diff-line-num" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1389
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<td class="new_line diff-line-num" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1403
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1403" 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>
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<td class="old_line diff-line-num old" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1390
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<td class="new_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(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="LC1390" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">with</span></span><span class="idiff deletion"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion">open</span></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 class="idiff deletion">)</span></span><span class="idiff deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">as</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">mblocks</span></span><span class="p"><span class="idiff right deletion">:</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1391
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<td class="new_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(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="LC1391" class="line" lang="python"> <span class="idiff left deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">for</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff right deletion">line</span></span> <span class="ow" style="font-weight: 600;">in</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="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1392
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<td class="new_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(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="LC1392" class="line" lang="python"> <span class="idiff left deletion"> </span><span class="k" style="font-weight: 600;"><span class="idiff deletion">if</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">line</span></span><span class="p"><span class="idiff deletion">[</span></span><span class="mi" style="color: #099;"><span class="idiff deletion">0</span></span><span class="p"><span class="idiff deletion">]</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!=</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;"><span class="idiff deletion">">"</span></span><span class="idiff deletion"> </span><span class="ow" style="font-weight: 600;"><span class="idiff deletion">and</span></span><span class="idiff deletion"> </span><span class="nb" style="color: #0086b3;"><span class="idiff deletion">len</span></span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">line</span></span><span class="p"><span class="idiff deletion">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion">rstrip</span></span><span class="p"><span class="idiff right deletion">()</span>)</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="1393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1393
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<td class="new_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(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="LC1393" class="line" lang="python"> <span class="idiff left right deletion"> </span><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>
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<td class="old_line diff-line-num old" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1394
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<td class="new_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(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="LC1394" class="line" lang="python"> <span class="idiff left right deletion"> </span><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="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1395
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<td class="new_line diff-line-num old" data-linenumber="1404" style="width: 35px; color: rgba(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="LC1395" class="line" lang="python"> <span class="idiff left right deletion"> </span><span class="k" style="font-weight: 600;">break</span></span>
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<td class="old_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">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1404" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left addition">mblocks_seqs</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">SeqIO</span></span><span class="p"><span class="idiff addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">parse</span></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 class="idiff addition">,</span></span><span class="idiff addition"> </span><span class="s" style="color: #d14;"><span class="idiff addition">"fasta"</span></span><span class="p"><span class="idiff right addition">)</span></span></span>
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<td class="old_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">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1405" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left addition">for</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">seq</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mblocks<span class="idiff right addition">_seqs</span></span><span class="p">:</span></span>
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<td class="old_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">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1406" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left addition">if</span></span><span class="idiff addition"> </span><span class="nb" style="color: #0086b3;"><span class="idiff addition">len</span></span><span class="p"><span class="idiff addition">(</span></span><span class="n" style="color: #333;"><span class="idiff right addition">seq</span></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="new_line diff-line-num new" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1407
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1407" 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>
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<td class="old_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">
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<td class="new_line diff-line-num new" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1408
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1408" 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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1409" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="old_line diff-line-num" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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<td class="new_line diff-line-num" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1410
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1410" 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>
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<td class="old_line diff-line-num old" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1397
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<td class="new_line diff-line-num old" data-linenumber="1411" style="width: 35px; color: rgba(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="LC1397" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;"><span class="idiff left deletion">tempfile</span></span><span class="p"><span class="idiff right deletion">.</span></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>
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<td class="old_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">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1411" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</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>
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<td class="old_line diff-line-num" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1398
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<td class="new_line diff-line-num" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1412" 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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1399
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<td class="new_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1413
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1413" 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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1400
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<td class="new_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1414" 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="diff-line-num unfold js-unfold old_line" data-linenumber="1450" style="width: 35px; color: rgba(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="1464" style="width: 35px; color: rgba(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">@@ -1450,9 +1464,9 @@ Please verify recruited genomes are all strain of interest""")</td>
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1450
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<td class="new_line diff-line-num" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1464
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1464" 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="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1451
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1465" 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;">"Aligned %d genomes in %.2f seconds"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">totseqs</span><span class="p">,</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>
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<td class="old_line diff-line-num" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1452
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1466" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#cleanup</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1453
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<td class="new_line diff-line-num old" data-linenumber="1467" style="width: 35px; color: rgba(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="LC1453" class="line" lang="python"> <span class="n" style="color: #333;">rmfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left deletion">glob</span></span><span class="p"><span class="idiff right deletion">.</span></span><span class="n" style="color: #333;">glob</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;">"*.aln"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); 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="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1467
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1467" class="line" lang="python"> <span class="n" style="color: #333;">rmfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</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;">"*.aln"</span><span class="p">))</span></span>
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1454
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<td class="new_line diff-line-num" data-linenumber="1468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1468
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1468" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#rmfiles2 = glob.glob(outputDir+os.sep+"blocks/b*/*")</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1455
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<td class="new_line diff-line-num old" data-linenumber="1469" style="width: 35px; color: rgba(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="LC1455" class="line" lang="python"> <span class="n" style="color: #333;">rmfiles3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left deletion">glob</span></span><span class="p"><span class="idiff right deletion">.</span></span><span class="n" style="color: #333;">glob</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;">"blocks/b*"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); 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="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1469
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1469" class="line" lang="python"> <span class="n" style="color: #333;">rmfiles3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">glob</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;">"blocks/b*"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1456
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<td class="new_line diff-line-num" data-linenumber="1470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1470
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1470" 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;">rmfiles</span><span class="p">:</span></span>
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1457
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1471
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1471" 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="n" style="color: #333;">f</span><span class="p">)</span></span>
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1458
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1472
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1472" 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;">rmfiles3</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1491" style="width: 35px; color: rgba(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="1505" style="width: 35px; color: rgba(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">@@ -1491,13 +1505,13 @@ Please verify recruited genomes are all strain of interest""")</td>
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1491
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<td class="new_line diff-line-num" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1505
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1505" 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;">VERBOSE</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;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%s.delta"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">)):</span></span>
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<td class="old_line diff-line-num" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1492
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<td class="new_line diff-line-num" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1506
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1506" 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;">"%s.delta"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">))</span></span>
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1493
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<td class="new_line diff-line-num" data-linenumber="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1507
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1507" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1494
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<td class="new_line diff-line-num old" data-linenumber="1508" style="width: 35px; color: rgba(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="LC1494" 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;"><span class="idiff left deletion">glob</span></span><span class="p"><span class="idiff right deletion">.</span></span><span class="n" style="color: #333;">glob</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;">"*.reps"</span><span class="p">)):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1508
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1508" 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;">glob</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;">"*.reps"</span><span class="p">)):</span></span>
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1495
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<td class="new_line diff-line-num" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1509
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1509" 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;">VERBOSE</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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1496
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<td class="new_line diff-line-num" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1510
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1510" 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="n" style="color: #333;">f</span><span class="p">)</span></span>
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1497
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<td class="new_line diff-line-num" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1511
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1511" class="line" lang="python"></span>
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1498
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<td class="new_line diff-line-num old" data-linenumber="1512" style="width: 35px; color: rgba(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="LC1498" 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;"><span class="idiff left deletion">glob</span></span><span class="p"><span class="idiff right deletion">.</span></span><span class="n" style="color: #333;">glob</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;">"*.ref"</span><span class="p">)):</span></span>
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1499
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<td class="new_line diff-line-num old" data-linenumber="1512" style="width: 35px; color: rgba(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="LC1499" 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;">VERBOSE</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;">exists</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1500
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<td class="new_line diff-line-num old" data-linenumber="1512" style="width: 35px; color: rgba(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="LC1500" 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="n" style="color: #333;">f</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); 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="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1512
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1512" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition"># </span>for f in glob(os.path.join(outputDir, "*.ref")):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); 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="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1513
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1513" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition"># </span>if not VERBOSE and os.path.exists(f):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1514
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1514" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition"># </span>os.remove(f)</span></span>
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1501
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<td class="new_line diff-line-num" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1515" class="line" lang="python"></span>
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1502
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<td class="new_line diff-line-num" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1516
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1516" 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;">VERBOSE</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;">exists</span><span class="p">(</span><span class="s" style="color: #d14;">"%s/psnn.ini"</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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1503
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<td class="new_line diff-line-num" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1517" 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;">"%s/psnn.ini"</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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<a href="https://salsa.debian.org/med-team/parsnp/-/compare/438fe8f7e6a08fbfbde951f3fa71281d90ddd78f...ca0f9296e126cd1de30793cc0a35d70f7f6bb834#ee78169a89b940136b8c2936e3018e3d83272ed7"><strong>src/parsnp.cpp</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -995,20 +995,39 @@ void Aligner::writeOutput(string psnp,vector<float>& coveragerow)</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lasthdr1</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp"> <span class="n" style="color: #333;">seqstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">laststart</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC997" class="line" lang="cpp"> <span class="p">}</span></span>
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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="LC998" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">mums</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">isforward</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">)</span></span>
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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="LC999" class="line" lang="cpp"> <span class="p">{</span></span>
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1000
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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="LC1000" class="line" lang="cpp"> <span class="n" style="color: #333;">xmfafile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"- cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1001
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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="LC1001" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">recomb_filter</span><span class="p">)</span></span>
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998
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC998" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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999
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC999" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">mums</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">isforward</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">)</span></span>
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1002
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1000" class="line" lang="cpp"> <span class="p">{</span></span>
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1003
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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="LC1003" class="line" lang="cpp"> <span class="n" style="color: #333;">clcbfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"- cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1001
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1001" class="line" lang="cpp"> <span class="n" style="color: #333;">xmfafile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"- cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1002
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1002" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">recomb_filter</span><span class="p">)</span></span>
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1003
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"> <span class="p">{</span></span>
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1004
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">clcbfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"- cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1005
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="p">}</span></span>
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1004
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1006
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1006" class="line" lang="cpp"> <span class="p">}</span></span>
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1005
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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="LC1005" class="line" lang="cpp"> <span class="p">}</span></span>
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1006
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<td class="new_line diff-line-num old" data-linenumber="1007" style="width: 35px; color: rgba(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="LC1006" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1007
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<td class="new_line diff-line-num old" data-linenumber="1007" style="width: 35px; color: rgba(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="LC1007" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1008
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<td class="new_line diff-line-num old" data-linenumber="1007" style="width: 35px; color: rgba(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="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">xmfafile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+ cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1009
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<td class="new_line diff-line-num old" data-linenumber="1007" style="width: 35px; color: rgba(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="LC1009" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">recomb_filter</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1007
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1010
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<td class="new_line diff-line-num" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1008
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> <span class="p">{</span></span>
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1011
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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="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">clcbfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+ cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1009
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">xmfafile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+ cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1010
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">recomb_filter</span><span class="p">)</span></span>
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1011
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1012
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">clcbfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+ cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1013
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="p">}</span></span>
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1014
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="p">}</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1015
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1016
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1016" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">mums</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">isforward</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">)</span></span>
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1017
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1017" class="line" lang="cpp"> <span class="p">{</span></span>
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1018
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"> <span class="n" style="color: #333;">xmfafile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"- cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s1"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">hdr1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">mums</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1019
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">recomb_filter</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1020
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1021
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">clcbfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"- cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1022
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1025
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1026
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">xmfafile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+ cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">((</span><span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"s1"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">hdr1</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">recomb_filter</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"> <span class="n" style="color: #333;">clcbfile</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"+ cluster"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">hdr1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":p"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1012" style="width: 35px; color: rgba(0,0,0,0.3); 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="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1030
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="p">}</span></span>
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1012
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<td class="new_line diff-line-num" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1031
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1031" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1013
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<td class="new_line diff-line-num" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1032
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1032" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1014
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<td class="new_line diff-line-num" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1033
</td>
<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1033" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s1s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();)</span></span>
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