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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/perm">Debian Med / perm</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/perm/-/commit/b58c0975e0d43f9783554afe8ee9b48eeaf90d84">b58c0975</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-03T00:31:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/perm/-/commit/d6e9cdfddd478555c3c02448bcd65e8342da3539">d6e9cdfd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-03T00:41:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/copyright: Minor Fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/perm/-/commit/075178ffb8fb1ac8476e2056a48587a64d647163">075178ff</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-03T00:44:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/tests/run-unit-test: Minor fix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/perm/-/commit/0f28975f9628428774265176a1d1ac3fb1745231">0f28975f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-03T00:44:59+05:30</i>
</div>
<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
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#52516601f6bd2e588a6fffc8c23daa306f620201">
debian/patches/fix-buffer-overflow.patch
</a>
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/perm/-/compare/8034f60434e71f71eaa180faf417cc63a2871e87...0f28975f9628428774265176a1d1ac3fb1745231#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">perm (0.4.0-6) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">perm (0.4.0-6) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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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"> * Add testdata</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Sun, 01 Aug 2021 19:32:02 +0530</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> [ Shruti Sridhar ]</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * d/tests/data: Add testdata</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/tests: Add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/example: Install test data as example</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * d/docs: Install d/README.* and d/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> as documents</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * d/p/hardening.patch: Add CPPFLAGS which helped detect</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> buffer overflow</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * d/copyright: Test data has been written by Shruti, mentioning</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> them in copyright for the same</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * d/p/fix-buffer-overflow.patch: Use strlcpy from libbsd-dev</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> instead of strncpy in order to fix buffer overflow</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * d/control: Add B-D on libbsd-dev</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Tue, 03 Aug 2021 00:31:10 +0530</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">perm (0.4.0-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/perm/-/compare/8034f60434e71f71eaa180faf417cc63a2871e87...0f28975f9628428774265176a1d1ac3fb1745231#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -12,7 +12,7 @@ Copyright: (c) 2012-2014 Hyun Soon Gweon <hyugwe@ceh.ac.uk></td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> 2014-2017 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">License: Apache-2.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Files: debian/tests/data</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Files: debian/tests/data<span class="idiff left right">/*</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Copyright: Shruti Sridhar <shruti.sridhar99@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">License: Apache-2.0</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/perm/-/compare/8034f60434e71f71eaa180faf417cc63a2871e87...0f28975f9628428774265176a1d1ac3fb1745231#52516601f6bd2e588a6fffc8c23daa306f620201"><strong>debian/patches/fix-buffer-overflow.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use strlcpy from libbsd-dev instead of strncpy in order to avoid buffer overflow</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2021-08-03</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/makefile</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -2,7 +2,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/perm/-/compare/8034f60434e71f71eaa180faf417cc63a2871e87...0f28975f9628428774265176a1d1ac3fb1745231#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -14,4 +14,5 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell">perm Ref.fasta Reads.fasta <span class="nt" style="color: #000080;">-v</span> 100 <span class="nt" style="color: #000080;">-A</span> <span class="nt" style="color: #000080;">-o</span> out.sam </span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"out.sam"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS test"</span></span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"out.sam"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS test"</span></span></pre>
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