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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/soapaligner">Debian Med / soapaligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/-/commit/4bebafbff0d34b55b44be80d0db860bbf009b9a5">4bebafbf</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-14T17:05:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/p/gcc-10.patch: Fix compilation with GCC 10.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/-/commit/8aa0280228b036471dd3664fbab141a4b3d348d0">8aa02802</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-14T17:05:22+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/-/commit/b5b05003f2f10f09e1cdb2771e5d5e2e94c5bd49">b5b05003</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-14T17:05:35+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump debhelper-compat version to 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapaligner/-/commit/45420b6339098b64e3755be40fdc7d8c65a87f22">45420b63</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-14T17:06:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#61346daf162ff89209d7c978642f1eef5cd45723">
<span class="new-file">
+
debian/patches/gcc-10.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/soapaligner/-/compare/331cf08ce13bd48a121c95fe5e7b0fb4273b08a0...45420b6339098b64e3755be40fdc7d8c65a87f22#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">soapaligner (2.20-5) 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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<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">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * d/p/gcc-10.patch: Fix compilation with GCC 10.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - Thank you, Logan Rosen</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Declare compliance with policy 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Bump debhelper-compat version to 13</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Thu, 14 Jan 2021 17:05:45 +0530</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">soapaligner (2.20-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/soapaligner/-/compare/331cf08ce13bd48a121c95fe5e7b0fb4273b08a0...45420b6339098b64e3755be40fdc7d8c65a87f22#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">@@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>)</span>
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<pre style="margin: 0;">-<span id="LC7" 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="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/soapaligner</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Homepage: https://web.archive.org/web/20190127081222/http://soap.genomics.org.cn/soapaligner.html</span>
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<li id="61346daf162ff89209d7c978642f1eef5cd45723">
<a href="https://salsa.debian.org/med-team/soapaligner/-/compare/331cf08ce13bd48a121c95fe5e7b0fb4273b08a0...45420b6339098b64e3755be40fdc7d8c65a87f22#61346daf162ff89209d7c978642f1eef5cd45723"><strong>debian/patches/gcc-10.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use extern to fix gcc-10 FTBFS</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Logan Rosen <logan@ubuntu.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=979681</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-01-14</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/extratools.h</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/extratools.h</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -59,12 +59,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> HITITEM *itemList;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> }HITTABLE;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BWT * occBwt;</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;">-HASHTABLE * occHashtable;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-unsigned int * occCollector;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-unsigned int occCollected;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern BWT * occBwt;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern HASHTABLE * occHashtable;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern unsigned int * occCollector;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern unsigned int occCollected;</span></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 class="gd" style="color: #000; background-color: #fdd;">-FILE * textPositionFile;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extern FILE * textPositionFile;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> void registerTPFile(FILE * filePtr,unsigned int searchMode);</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> void registerQIndex(unsigned int queryIndex);</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/extratools.c</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/extratools.c</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -5,6 +5,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> // Hash Table</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> // All things like those</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+BWT * occBwt;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+HASHTABLE * occHashtable;</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;">+unsigned int * occCollector;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+unsigned int occCollected;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+FILE * textPositionFile;</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> void LoadLookupTable(LOOKUPTABLE * lookupTable, const char * fileName, const int tableSize) {</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> (*lookupTable).tableSize = tableSize;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> unsigned long long NR_TOP = 1 << (tableSize * 2);</span></pre>
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<a href="https://salsa.debian.org/med-team/soapaligner/-/compare/331cf08ce13bd48a121c95fe5e7b0fb4273b08a0...45420b6339098b64e3755be40fdc7d8c65a87f22#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">@@ -2,3 +2,4 @@ compiler_options.patch</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">linkerror.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">UsageDoublette.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">spelling.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">gcc-10.patch</span></pre>
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