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<h3>

Étienne Mollier pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/c64dced563cb97508ea181ff4c0afe45f590d38f">c64dced5</a></strong>

<div>

<span>by Etienne Mollier</span>

<i>at 2020-09-07T21:08:19+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: register with uppercase 'e' acute

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/39affaf3a00b376e3290dbcc03ff4dec72088796">39affaf3</a></strong>

<div>

<span>by Etienne Mollier</span>

<i>at 2020-09-07T21:09:43+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: bump deps to ncbi-blast+ >= 2.10.0-2

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/abc066528bde155e26a369beec8563b73a9855b2">abc06652</a></strong>

<div>

<span>by Etienne Mollier</span>

<i>at 2020-09-08T21:15:43+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bump build-dep on ncbi-blast+ 2.10.0-3

2.10.0-2 had a bug on amd64 architecture

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/414e0f60c97da133064ba29befec8c7184d7fcda">414e0f60</a></strong>

<div>

<span>by Etienne Mollier</span>

<i>at 2020-09-08T21:17:53+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">removed blastdbv4-test.patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-biopython/-/commit/9c4c52a4df0dd86c77057eeea5f9b50414552f68">9c4c52a4</a></strong>

<div>

<span>by Etienne Mollier</span>

<i>at 2020-09-08T22:55:43+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">blastdbv4-impl.patch applied-upstream

</pre>

</li>

</ul>

<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

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<li class="file-stats">

<a href="#d6ceb9f3cf749ec9fb61b57898aa3dd728569ca1">

debian/patches/blastdbv4-impl.patch

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<li class="file-stats">

<a href="#10cd05057caa55b09ff4347c75ee49a3e93ced42">

<span class="deleted-file">

−

debian/patches/blastdbv4-test.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.77</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">4</span><span class="p">)</span> <span class="n" style="color: #333;">UNRELEASED</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>

</pre>

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

</pre>

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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="mosel">  <span class="p">*</span> <span class="n" style="color: #333;">Bumped</span> <span class="n" style="color: #333;">build</span> <span class="n" style="color: #333;">requirement</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">ncbi</span><span class="p">-</span><span class="n" style="color: #333;">blast</span><span class="p">+</span> <span class="m" style="color: #099;">2.10.0</span><span class="p">-</span><span class="m" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">greater</span><span class="p">,</span></span>

</pre>

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel">  <span class="p">*</span> <span class="n" style="color: #333;">Removed</span> <span class="n" style="color: #333;">patch</span> <span class="n" style="color: #333;">against</span> <span class="n" style="color: #333;">tests</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">makeblastdb</span> <span class="n" style="color: #333;">bug</span> <span class="n" style="color: #333;">around</span> <span class="n" style="color: #333;">on</span> <span class="m" style="color: #099;">32</span> <span class="n" style="color: #333;">bit</span> <span class="n" style="color: #333;">archs</span><span class="p">.</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">--</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">É</span><span class="n" style="color: #333;">tienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p"><</span><span class="n" style="color: #333;">etienne</span><span class="p">.</span><span class="n" style="color: #333;">mollier</span><span class="p">@</span><span class="n" style="color: #333;">mailoo</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span>  <span class="n" style="color: #333;">Mon</span><span class="p">,</span> <span class="m" style="color: #099;">07</span> <span class="n" style="color: #333;">Sep</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">20</span><span class="p">:</span><span class="m" style="color: #099;">37</span><span class="p">:</span><span class="m" style="color: #099;">27</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></span>

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">biopython</span> <span class="p">(</span><span class="m" style="color: #099;">1.77</span><span class="p">+</span><span class="n" style="color: #333;">dfsg</span><span class="p">-</span><span class="m" style="color: #099;">3</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel">  <span class="p">[</span> <span class="n" style="color: #333;">Etienne</span> <span class="n" style="color: #333;">Mollier</span> <span class="p">]</span></span>

</pre>

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</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ Source: python-biopython</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Charles Plessy <plessy@debian.org>,</span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">           Andreas Tille <tille@debian.org>,</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">           <span class="idiff left right">E</span>tienne Mollier <etienne.mollier@mailoo.org></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">           <span class="idiff left right">É</span>tienne Mollier <etienne.mollier@mailoo.org></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: python</span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 12),</td>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">               fasttree <!nocheck>,</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">               mafft <!nocheck>,</span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">               muscle <!nocheck>,</span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">               ncbi-blast+ <!nocheck>,</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">               ncbi-blast+ <span class="idiff left right">(>= 2.10.0-3) </span><!nocheck>,</span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">               phylip <!nocheck>,</span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">               phyml [any-amd64 any-i386] <!nocheck>,</span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">               prank <!nocheck>,</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(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">@@ -58,7 +58,7 @@ Depends: ${python3:Depends},</td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">         ${misc:Depends},</span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">         python3-reportlab</span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">Recommends: python-biopython-doc (= ${source:Version}),</span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">            ncbi-blast+</span>

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

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">            ncbi-blast+<span class="idiff left right"> (>= 2.10.0-3)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">Suggests: python3-tk,</span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">          bwa,</span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">          clustalo,</span>

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<li id="d6ceb9f3cf749ec9fb61b57898aa3dd728569ca1">

<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68#d6ceb9f3cf749ec9fb61b57898aa3dd728569ca1"><strong>debian/patches/blastdbv4-impl.patch</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(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">@@ -5,7 +5,8 @@ Description: Implement BLAST database version 4 switch</td>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> as well, hence a separation of the implementation and test.</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">Forwarded: https://github.com/biopython/biopython/pull/2987</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2020-06-10</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Applied-Upstream: 1.79</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2020-09-08</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">---</span></span>

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<pre style="margin: 0;"> <span id="LC11" 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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Bio/Blast/Applications.py</span></span>

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<li id="10cd05057caa55b09ff4347c75ee49a3e93ced42">

<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68#10cd05057caa55b09ff4347c75ee49a3e93ced42"><strong>debian/patches/blastdbv4-test.patch</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: adapt makeblastdb wrapper test for 32 bits architecture</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> This patch works around issues with testing the wrapper to makeblastdb, which</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> fails to execute on 32 bit CPU architectures due to starvation of the virtual</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> memory address space.  This issue is apparently specific to the construction</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> of BLAST databases in version 5 format, and does not occur when falling back</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> to version 4.  This requires the wrapper to know about falling back to version</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> 4, which is addressed by another patch.</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">Author: Étienne Mollier <etienne.mollier@mailoo.org></span></span>

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9

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/960756</span></span>

</pre>

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10

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 2020-06-10</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- python-biopython.orig/Tests/test_NCBI_BLAST_tools.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ python-biopython/Tests/test_NCBI_BLAST_tools.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -217,6 +217,7 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">         global exe_names</span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">         cline = Applications.NcbimakeblastdbCommandline(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">             exe_names["makeblastdb"],</span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            blastdb_version=4,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">             input_file="GenBank/NC_005816.faa",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff">             dbtype="prot",</span>

</pre>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff">             hash_index=True,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -228,7 +229,8 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff">         self.assertEqual(</span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">             str(cline),</span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff">             _escape_filename(exe_names["makeblastdb"])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            + " -dbtype prot -in GenBank/NC_005816.faa"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            + " -blastdb_version 4"</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            " -dbtype prot -in GenBank/NC_005816.faa"</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="31" 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>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff">             " -parse_seqids -hash_index -max_file_sz 20MB"</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff">             " -taxid 10",</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff">         )</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="34" 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="LC34" class="line" lang="diff"><span class="p">@@ -263,6 +265,7 @@</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff">         global exe_names</span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff">         cline = Applications.NcbimakeblastdbCommandline(</span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff">             exe_names["makeblastdb"],</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

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

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            blastdb_version=4,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

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

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff">             input_file="GenBank/NC_005816.fna",</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" 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">

40

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

</td>

<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="diff">             dbtype="nucl",</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="41" 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">

41

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

</td>

<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="diff">             hash_index=True,</span>

</pre>

</td>

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

42

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

</td>

<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="diff"><span class="p">@@ -274,7 +277,8 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="43" 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">

43

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

</td>

<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="diff">         self.assertEqual(</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="44" 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">

44

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

</td>

<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="diff">             str(cline),</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" 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">

45

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

</td>

<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="diff">             _escape_filename(exe_names["makeblastdb"])</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="46" 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">

46

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

</td>

<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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            + " -dbtype nucl -in GenBank/NC_005816.fna"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="47" 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">

47

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

</td>

<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="gi" style="color: #000; background-color: #dfd;">+            + " -blastdb_version 4"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="48" 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">

48

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

</td>

<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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            " -dbtype nucl -in GenBank/NC_005816.fna"</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="49" 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">

49

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

</td>

<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="diff">             " -parse_seqids -hash_index -max_file_sz 20MB"</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="50" 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">

50

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

</td>

<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="diff">             " -taxid 10",</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="51" 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">

51

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff">         )</span></pre>

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</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">remove_mathml-qname.patch</span>

</pre>

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

2

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

2

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

</pre>

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

3

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

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">blastdbv4-impl.patch</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">blastdbv4-test.patch</span>

</pre>

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5

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">71d9f4e2398d542d04001eabb1b467a6f3fdeecf.patch</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">1c3504736d41e6f6d0931e6f2685f95e486b27c8.patch</span></pre>

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