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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/sibelia">Debian Med / sibelia</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/-/commit/92d4b42f6e06ecb1a4701ed4f81d5478a6bb041d">92d4b42f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T06:16:04+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/-/commit/7e4092a684cc97801cf43877725662a93b29bdd4">7e4092a6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T07:34:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix LAGAN_DIR
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sibelia/-/commit/a2784e346df07096e0352f27f24f2a5d2e752868">a2784e34</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-03-26T07:38:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing line
</pre>
</li>
</ul>
<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#338b7589d65fa5e99e5ebe5f500dba8860ef625d">
debian/patches/use_debian_packaged_lagan.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/sibelia/-/compare/95f9bf96514cbb8bfdc6584223c58f0ef3aba719...a2784e346df07096e0352f27f24f2a5d2e752868#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">@@ -15,6 +15,35 @@ Copyright: 2011-2018 Saint-Petersburg Academic University</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> Ilya Minkin, Nikolay Vyahhi, Mikhail Kolmogorov, Son Pham</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">License: GPL-2</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Files: src/resource.cpp</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Copyright: 2001 Robert Penner</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> modification, are permitted provided that the following conditions are met:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> - Redistributions of source code must retain the above copyright notice, this</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> list of conditions and the following disclaimer.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> - Redistributions in binary form must reproduce the above copyright notice,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> this list of conditions and the following disclaimer in the documentation</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> and/or other materials provided with the distribution.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> - Neither the name of the author nor the names of contributors may be used to</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> endorse or promote products derived from this software without specific</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> prior written permission.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> POSSIBILITY OF SUCH DAMAGE.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Copyright: 2019 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">License: GPL-2</span>
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<br>
</li>
<li id="338b7589d65fa5e99e5ebe5f500dba8860ef625d">
<a href="https://salsa.debian.org/med-team/sibelia/-/compare/95f9bf96514cbb8bfdc6584223c58f0ef3aba719...a2784e346df07096e0352f27f24f2a5d2e752868#338b7589d65fa5e99e5ebe5f500dba8860ef625d"><strong>debian/patches/use_debian_packaged_lagan.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="13" 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">@@ -13,3 +13,14 @@ Description: Use Debian packaged lagan</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> install(PROGRAMS csibelia/C-Sibelia.py DESTINATION bin)</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> install(PROGRAMS annotation/snpEffAnnotate.py DESTINATION bin)</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> install(DIRECTORY annotation/snpEff DESTINATION ${LIB_DIR})</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/csibelia/C-Sibelia.py</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;">+++ b/src/csibelia/C-Sibelia.py</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span> LINE_LENGTH = 60</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> MINIMUM_CONTEXT_SIZE = 30</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> BLOCKS_FILE = 'blocks_sequences.fasta'</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> INSTALL_DIR = os.path.dirname(os.path.abspath(__file__))</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LAGAN_DIR = os.path.join(INSTALL_DIR, '..', 'lib', 'Sibelia', 'lagan')</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LAGAN_DIR = '/usr/bin'</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> os.environ['LAGAN_DIR'] = LAGAN_DIR</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> FastaRecord = collections.namedtuple('FastaRecord', ['seq', 'description', 'id'])</span></pre>
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