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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/parsnp">Debian Med / parsnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/b30b424344d0f7284600757ed4fa65fcbe061157">b30b4243</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-01T18:13:50+05:30</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/2a23b71a8e230b0cff0e487b80e6c908b16c11da">2a23b71a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-01T18:13:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.4+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/a469129f1f7b15a7f8015597f5fe85a3f3eec42c">a469129f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-01T18:13:53+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.5.4+dfsg'
Update to upstream version '1.5.4+dfsg'
with Debian dir 216dd80a46537771fa1411f80b81e9865ebaeaec</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/5127f54d750172905ce96a099301b8eb3e5379e9">5127f54d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-01T18:13:53+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/parsnp/-/commit/7bf28601bd95efc84dfc48fd0e910799032b984a">7bf28601</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-01T18:14:10+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#3849e3531855982fc7f5e63b3b17488714940ae3">
parsnp
</a>
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/f57542858423f6082acfd0bce143d078587b2ed0...7bf28601bd95efc84dfc48fd0e910799032b984a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">parsnp (1.5.4+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Tue, 01 Dec 2020 18:14:10 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">parsnp (1.5.3+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team Upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/f57542858423f6082acfd0bce143d078587b2ed0...7bf28601bd95efc84dfc48fd0e910799032b984a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libmuscle-dev</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/parsnp</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/parsnp.git</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html</span>
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<li id="3849e3531855982fc7f5e63b3b17488714940ae3">
<a href="https://salsa.debian.org/med-team/parsnp/-/compare/f57542858423f6082acfd0bce143d078587b2ed0...7bf28601bd95efc84dfc48fd0e910799032b984a#3849e3531855982fc7f5e63b3b17488714940ae3"><strong>parsnp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ import signal</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.5.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.5.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">reroot_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="c1" style="color: #998; font-style: italic;">#use --midpoint-reroot</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1317,6 +1317,7 @@ Please verify recruited genomes are all strain of interest""")</td>
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="python"> <span class="n" style="color: #333;">bedfile_dict</span><span class="p">[</span><span class="n" style="color: #333;">srpos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">REC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.3f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">srpos</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">block_spos</span><span class="p">,</span><span class="nb" style="color: #0086b3;">eval</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="python"> <span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="python"> <span class="n" style="color: #333;">chr_spos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ref_seqs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_seqs</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">block_spos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">chr_spos</span><span class="p">:</span></span>
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1322
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="python"> <span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_seqs</span><span class="p">[</span><span class="n" style="color: #333;">cs</span><span class="p">]</span></span>
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