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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/adapterremoval">Debian Med / adapterremoval</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/35b394ebcbcef6525e4f9672829638bf95be30ef">35b394eb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-10T15:42:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix build on some architectures
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/6c2d8de0c6e049908353991a5de1b4cd1925a618">6c2d8de0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-10T15:43:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Submit.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/f9ec325b2a56b2912ff409e22756014a48d46ea0">f9ec325b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-10T15:54:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Complete patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/adapterremoval/commit/039cf0dca33ed375589dfa45ccb1f4fe0827511e">039cf0dc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-10T15:58:55+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#75cae4bffb0a01f8c7aac373e54895ac8abbc31b">
<span class="new-file">
+
debian/patches/fix_conversion.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525...039cf0dca33ed375589dfa45ccb1f4fe0827511e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">adapterremoval (2.3.1-3) 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"> * Fix build on some architectures</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #923772</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Submit.</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"> -- Andreas Tille <tille@debian.org> Fri, 10 Jan 2020 15:43:41 +0100</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">adapterremoval (2.3.1-2) 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 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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Build-Depends: markdown instead of python-markdown</span>
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<li id="75cae4bffb0a01f8c7aac373e54895ac8abbc31b">
<a href="https://salsa.debian.org/med-team/adapterremoval/compare/bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525...039cf0dca33ed375589dfa45ccb1f4fe0827511e#75cae4bffb0a01f8c7aac373e54895ac8abbc31b"><strong>debian/patches/fix_conversion.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix build on some architectures</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/923772</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Fri, 10 Jan 2020 15:39:08 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/src/alignment_tables.cpp</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/alignment_tables.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -82,7 +82,7 @@</span> std::vector<phred_scores> calculate_phre</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const char IDENTICAL_NTS[PHRED_TABLE_SIZE] = {</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const signed char IDENTICAL_NTS[PHRED_TABLE_SIZE] = {</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> 0x22, 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> 0x22, 0x22, 0x24, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -179,7 +179,7 @@</span> const char IDENTICAL_NTS[PHRED_TABLE_SIZ</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> 0x7d, 0x7d, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e, 0x7e,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-const char DIFFERENT_NTS[PHRED_TABLE_SIZE] = {</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+const signed char DIFFERENT_NTS[PHRED_TABLE_SIZE] = {</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> 0x22, 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> 0x23, 0x23, 0x22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/alignment_tables.hpp</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/alignment_tables.hpp</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -37,7 +37,7 @@</span> const size_t PHRED_TABLE_SIZE = 8836;</span>
</pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> * Position is calculated as phred_1 * (MAX_PHRED_SCORE + 1) + phred_2,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> * assuming that phred_1 >= phred_2.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extern const char IDENTICAL_NTS[PHRED_TABLE_SIZE];</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern const signed char IDENTICAL_NTS[PHRED_TABLE_SIZE];</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> * Table of Phred scores to assigned for mismatching positions during collapsing.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -45,7 +45,7 @@</span> extern const char IDENTICAL_NTS[PHRED_TA</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> * Position is calculated as phred_1 * (MAX_PHRED_SCORE + 1) + phred_2,</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> * assuming that phred_1 >= phred_2.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extern const char DIFFERENT_NTS[PHRED_TABLE_SIZE];</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern const signed char DIFFERENT_NTS[PHRED_TABLE_SIZE];</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> } // namespace ar</span></pre>
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<a href="https://salsa.debian.org/med-team/adapterremoval/compare/bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525...039cf0dca33ed375589dfa45ccb1f4fe0827511e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,3 +2,4 @@ adapt-benchmarking.patch</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">reduce_benchmark_length.patch</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">delete_adapterremoval1x_completely.patch</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fix_conversion.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/adapterremoval/compare/bb4d0b2f8d10602a43ffe9dfb2d21dcbfcb5b525...039cf0dca33ed375589dfa45ccb1f4fe0827511e#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">@@ -23,3 +23,4 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Bug-Database: https://github.com/MikkelSchubert/adapterremoval/issues</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Repository: https://github.com/MikkelSchubert/adapterremoval.git</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Repository-Browse: https://github.com/MikkelSchubert/adapterremoval</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Bug-Submit: https://github.com/MikkelSchubert/adapterremoval/issues/new</span></pre>
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