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<h3>
Bas Couwenberg pushed to branch master
at <a href="https://salsa.debian.org/med-team/libtfbs-perl">Debian Med / libtfbs-perl</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/19ac55578fbc98780632fa70de558469c0a0981c">19ac5557</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T19:48:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Import Debian changes 0.7.1-3.1
libtfbs-perl (0.7.1-3.1) unstable; urgency=medium
..
* Non-maintainer upload.
* No-change rebuild with PDL 2.0.57.
(closes: #993427)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/2a77e9312186ec829d052f46c68b9d935dcc986d">2a77e931</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2021-09-17T19:49:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/u/metadata: yamllint
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/984a0c2d1096b8f90f976c31ff494fa08b8a96d1">984a0c2d</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T19:51:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add gbp.conf to use pristine-tar & --source-only-changes by default.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/b7e084a36a7cbef3d5eef072cc9d0bac736475dc">b7e084a3</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T19:55:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/8909abb2b03c11e94326e3bf278e15a6bce2b8f6">8909abb2</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T19:55:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.6.0, no changes.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/597bbf885ade6470682eaa14c03065f1320a0201">597bbf88</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T20:08:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use AUTOPKGTEST_TMP instead of deprecated ADTTMP variable.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/05d0bcb4268ff08db06ae926027ac20e9d29abc1">05d0bcb4</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T20:12:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream metadata for GitHub repository.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/c1a3b8b1ea1a3c661e682317b126432877ceb6cd">c1a3b8b1</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T20:59:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update spelling errors path.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/7808efc4c55df14d288a63a5cc3d64374dcebc1c">7808efc4</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T20:59:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable PIE hardening flags too.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libtfbs-perl/-/commit/12f393b6900037f9dee9a7b68bed374bab49b15d">12f393b6</a></strong>
<div>
<span>by Bas Couwenberg</span>
<i>at 2021-09-17T20:59:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't override dh_auto_configure.
</pre>
</li>
</ul>
<h4>9 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>
</li>
<li class="file-stats">
<a href="#67df3adc98b97f87d2c73e4a05f22a987c3a5a7b">
<span class="new-file">
+
debian/gbp.conf
</span>
</a>
</li>
<li class="file-stats">
<a href="#5c7fe6d005e2933d378024ca390579ec62298c22">
<span class="new-file">
+
debian/patches/configure.patch
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#f70ccac42faeaba94dbbdf6f75111b35bde81797">
debian/patches/spelling-errors.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libtfbs-perl (0.7.1-4) UNRELEASED; urgency=medium</span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" 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="new_line diff-line-num new" 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"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * d/u/metadata: yamllint</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"> [ Bas Couwenberg ]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Add gbp.conf to use pristine-tar & --source-only-changes by default.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Bump Standards-Version to 4.6.0, no changes.</span>
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<td class="new_line diff-line-num new" 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="plaintext"> * Use AUTOPKGTEST_TMP instead of deprecated ADTTMP variable.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Update upstream metadata for GitHub repository.</span>
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<td class="new_line diff-line-num new" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Update spelling errors path.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Enable PIE hardening flags too.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Don't override dh_auto_configure.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> -- Bas Couwenberg <sebastic@debian.org> Fri, 17 Sep 2021 19:54:38 +0200</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">libtfbs-perl (0.7.1-3.1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> * Non-maintainer upload.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> * No-change rebuild with PDL 2.0.57.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> (closes: #993427)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> -- Bas Couwenberg <sebastic@debian.org> Sun, 05 Sep 2021 07:29:33 +0200</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">libtfbs-perl (0.7.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> [ Xavier Guimard ]</span>
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<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#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">@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> bioperl,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libwww-perl,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libdbi-perl</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.0</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6</span>.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libtfbs-perl</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libtfbs-perl.git</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://tfbs.genereg.net</span>
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<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#67df3adc98b97f87d2c73e4a05f22a987c3a5a7b"><strong>debian/gbp.conf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="conf">[<span class="n" style="color: #333;">DEFAULT</span>]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># The default name for the upstream branch is "upstream".</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Change it if the name is different (for instance, "master").</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="conf"><span class="n" style="color: #333;">upstream</span>-<span class="n" style="color: #333;">branch</span> = <span class="n" style="color: #333;">upstream</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># The default name for the Debian branch is "master".</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Change it if the name is different (for instance, "debian/unstable").</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="conf"><span class="n" style="color: #333;">debian</span>-<span class="n" style="color: #333;">branch</span> = <span class="n" style="color: #333;">master</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># git-import-orig uses the following names for the upstream tags.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Change the value if you are not using git-import-orig</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="conf"><span class="n" style="color: #333;">upstream</span>-<span class="n" style="color: #333;">tag</span> = <span class="n" style="color: #333;">upstream</span>/%(<span class="n" style="color: #333;">version</span>)<span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;"># Always use pristine-tar.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="conf"><span class="n" style="color: #333;">pristine</span>-<span class="n" style="color: #333;">tar</span> = <span class="n" style="color: #333;">True</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="conf">[<span class="n" style="color: #333;">buildpackage</span>]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="conf"><span class="n" style="color: #333;">pbuilder</span>-<span class="n" style="color: #333;">options</span> = --<span class="n" style="color: #333;">source</span>-<span class="n" style="color: #333;">only</span>-<span class="n" style="color: #333;">changes</span></span></pre>
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<li id="5c7fe6d005e2933d378024ca390579ec62298c22">
<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#5c7fe6d005e2933d378024ca390579ec62298c22"><strong>debian/patches/configure.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use environment variable to prevent interactive prompt.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Bas Couwenberg <sebastic@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/Makefile.PL</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/Makefile.PL</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -21,6 +21,7 @@</span> WriteMakefile(</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> sub get_sql_data {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> my $ans = "abc";</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $ans = $ENV{HAVE_MYSQL} if($ENV{HAVE_MYSQL});</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> do {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> print "Do you have write access to a MySQL database server? [n] ";</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> $ans=<STDIN>; chomp $ans;</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">spelling-errors.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">configure.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#f70ccac42faeaba94dbbdf6f75111b35bde81797"><strong>debian/patches/spelling-errors.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: Fix spelling errors.</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> hierachical -> hierarchical</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> occurence -> occurrence</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> acces -> access</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> aaccession -> accession</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">Author: Bas Couwenberg <sebastic@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff">--- a/TFBS/PatternGen/YMF.pm</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/PatternGen/YMF.pm</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -177,7 +177,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -177,7 +177,7 @@</span><span class="idiff left right"> sub _parse_stats_output{</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> my $motif =TFBS::PatternGen::YMF::Motif->new</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> (-word=>$word,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> -tags => {z_score=>$z_score,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +16,7 @@ Author: Bas Couwenberg <sebastic@debian.org></td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> 'expectation value'=>$expect,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> 'variance'=>$var}</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> );</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">@@ -190,4 +190,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -190,4 +190,4 @@</span><span class="idiff left right"> sub _parse_stats_output{</span></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>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>
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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">@@ -23,7 +25,7 @@ Author: Bas Couwenberg <sebastic@debian.org></td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+1;</span></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/TFBS/MatrixSet.pm</span></span>
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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/TFBS/MatrixSet.pm</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -763,7 +763,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -763,7 +763,7 @@</span><span class="idiff left right"> sub _build_cluster {</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> Title : cluster</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> Usage : $matrixset->cluster(%args)</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> Function: Clusters the matrices in the set</span>
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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">@@ -34,7 +36,7 @@ Author: Bas Couwenberg <sebastic@debian.org></td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> Args : Many:</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/Matrix/PFM.pm</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/Matrix/PFM.pm</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -366,7 +366,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -366,7 +366,7 @@</span><span class="idiff left right"> sub to_ICM {</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> # "pseudocounts" - standard pseudocount </span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> # correction, more suitable for </span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> # PFMs with large r column sums</span>
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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">@@ -43,3 +45,206 @@ Author: Bas Couwenberg <sebastic@debian.org></td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> # sample correction is not applied</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> -draw_error_bars # if true, adds error bars to each position</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/JASPAR.pm</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/JASPAR.pm</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -231,7 +231,7 @@</span> sub new {</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user's acces permissions for</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user's access permissions for</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> the database server.</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> =cut</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/JASPAR2.pm</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/JASPAR2.pm</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span> sub new {</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user acces permissions for</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user access permissions for</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> the database server.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> =cut</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -263,7 +263,7 @@</span> sub connect {</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> In place of NEWDATABASENAME, HOSTNAME, USERNAME and</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> PASSWORD use the actual values. PASSWORD and USERNAME</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- might be optional, depending on the users acces permissions</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ might be optional, depending on the users access permissions</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> for the database server.</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> =cut</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/JASPAR4.pm</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/JASPAR4.pm</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -188,7 +188,7 @@</span> sub new {</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user's acces permissions for</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user's access permissions for</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> the database server.</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> =cut</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/JASPAR5.pm</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/JASPAR5.pm</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -177,7 +177,7 @@</span> sub new {</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user's acces permissions for</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user's access permissions for</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> the database server.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> =cut</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/JASPAR6.pm</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/JASPAR6.pm</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span> sub new {</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user's acces permissions for</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user's access permissions for</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> the database server.</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> =cut</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/JASPAR7.pm</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/JASPAR7.pm</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="p">@@ -231,7 +231,7 @@</span> sub new {</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user's acces permissions for</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user's access permissions for</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> the database server.</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> =cut</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/lib/TFBS/DB/JASPAR2.pm</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/lib/TFBS/DB/JASPAR2.pm</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span> sub new {</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user acces permissions for</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user access permissions for</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> the database server.</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> =cut</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="p">@@ -263,7 +263,7 @@</span> sub connect {</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> In place of NEWDATABASENAME, HOSTNAME, USERNAME and</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> PASSWORD use the actual values. PASSWORD and USERNAME</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- might be optional, depending on the users acces permissions</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ might be optional, depending on the users access permissions</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> for the database server.</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> =cut</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/lib/TFBS/DB/JASPAR4.pm</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/lib/TFBS/DB/JASPAR4.pm</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="p">@@ -188,7 +188,7 @@</span> sub new {</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> use the actual values. PASSWORD and USERNAME might be</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- optional, depending on the user's acces permissions for</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ optional, depending on the user's access permissions for</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> the database server.</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> =cut</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/man3/TFBS::DB::JASPAR2.3pm</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/man3/TFBS::DB::JASPAR2.3pm</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="p">@@ -314,7 +314,7 @@</span> methods. Internal methods are preceded w</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> \& ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> \& In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> \& use the actual values. PASSWORD and USERNAME might be</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-\& optional, depending on the user acces permissions for</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\& optional, depending on the user access permissions for</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> \& the database server.</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> .Ve</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> .SS "create"</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="p">@@ -332,7 +332,7 @@</span> methods. Internal methods are preceded w</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> \& ("dbi:mysql:NEWDATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> \& In place of NEWDATABASENAME, HOSTNAME, USERNAME and</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> \& PASSWORD use the actual values. PASSWORD and USERNAME</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-\& might be optional, depending on the users acces permissions</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\& might be optional, depending on the users access permissions</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> \& for the database server.</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> .Ve</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> .SS "dbh"</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/LocalTRANSFAC.pm</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/LocalTRANSFAC.pm</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="p">@@ -105,7 +105,7 @@</span> ENDNOTICE</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> Title : get_Matrix_by_acc</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Function: fetches matrix data under the given TRANSFAC aaccession number</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Function: fetches matrix data under the given TRANSFAC accession number</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> from database and returns a TFBS::Matrix::* object</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> Returns : a TFBS::Matrix::* object; the exact type of the</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> object depending on the second argument (allowed</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/TFBS/DB/TRANSFAC.pm</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/TFBS/DB/TRANSFAC.pm</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="p">@@ -151,7 +151,7 @@</span> sub get_Matrix_by_ID {</span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> Title : get_Matrix_by_acc</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Function: fetches matrix data under the given TRANSFAC aaccession number</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Function: fetches matrix data under the given TRANSFAC accession number</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> from database and returns a TFBS::Matrix::* object</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> Returns : a TFBS::Matrix::* object; the exact type of the</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> object depending on the second argument (allowed</span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/lib/TFBS/DB/LocalTRANSFAC.pm</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/lib/TFBS/DB/LocalTRANSFAC.pm</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="p">@@ -105,7 +105,7 @@</span> ENDNOTICE</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> Title : get_Matrix_by_acc</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Function: fetches matrix data under the given TRANSFAC aaccession number</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Function: fetches matrix data under the given TRANSFAC accession number</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> from database and returns a TFBS::Matrix::* object</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> Returns : a TFBS::Matrix::* object; the exact type of the</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> object depending on the second argument (allowed</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/lib/TFBS/DB/TRANSFAC.pm</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/lib/TFBS/DB/TRANSFAC.pm</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="p">@@ -151,7 +151,7 @@</span> sub get_Matrix_by_ID {</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> Title : get_Matrix_by_acc</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> Usage : my $pfm = $db->get_Matrix_by_acc('V$CREB_01', 'PFM');</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Function: fetches matrix data under the given TRANSFAC aaccession number</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Function: fetches matrix data under the given TRANSFAC accession number</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> from database and returns a TFBS::Matrix::* object</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> Returns : a TFBS::Matrix::* object; the exact type of the</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> object depending on the second argument (allowed</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/man3/TFBS::DB::LocalTRANSFAC.3pm</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/man3/TFBS::DB::LocalTRANSFAC.3pm</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="p">@@ -188,7 +188,7 @@</span> TFBS::DB::LocalTRANSFAC is a read only d</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> .Vb 10</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> \& Title : get_Matrix_by_acc</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> \& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-\& Function: fetches matrix data under the given TRANSFAC aaccession number</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\& Function: fetches matrix data under the given TRANSFAC accession number</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> \& from database and returns a TFBS::Matrix::* object</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> \& Returns : a TFBS::Matrix::* object; the exact type of the</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> \& object depending on the second argument (allowed</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/man3/TFBS::DB::TRANSFAC.3pm</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/man3/TFBS::DB::TRANSFAC.3pm</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="p">@@ -217,7 +217,7 @@</span> retrieving a TFBS::Matrix::* object from</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> .Vb 10</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> \& Title : get_Matrix_by_acc</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> \& Usage : my $pfm = $db\->get_Matrix_by_acc(\*(AqV$CREB_01\*(Aq, \*(AqPFM\*(Aq);</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-\& Function: fetches matrix data under the given TRANSFAC aaccession number</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\& Function: fetches matrix data under the given TRANSFAC accession number</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> \& from database and returns a TFBS::Matrix::* object</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> \& Returns : a TFBS::Matrix::* object; the exact type of the</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> \& object depending on the second argument (allowed</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/blib/man3/TFBS::DB::JASPAR4.3pm</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/blib/man3/TFBS::DB::JASPAR4.3pm</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="p">@@ -256,7 +256,7 @@</span> methods. Internal methods are preceded w</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> \& ("dbi:mysql:DATABASENAME:HOSTNAME", "USERNAME", "PASSWORD")</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> \& In place of DATABASENAME, HOSTNAME, USERNAME and PASSWORD,</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> \& use the actual values. PASSWORD and USERNAME might be</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-\& optional, depending on the user\*(Aqs acces permissions for</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+\& optional, depending on the user\*(Aqs access permissions for</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> \& the database server.</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> .Ve</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> .SS "dbh"</span></pre>
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<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</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"># Enable hardening build flags</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all<span class="idiff left right">,-pie</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">CFLAGS += $(CPPFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">export HAVE_MYSQL=n</span></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">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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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">@@ -13,10 +13,6 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> rm --force Makefile Makefile.old</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> echo "n" | perl Makefile.PL INSTALLDIRS=vendor</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> $(MAKE) OPTIMIZE="$(CFLAGS)" LD_RUN_PATH="" OTHERLDFLAGS="$(LDFLAGS)"</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># Do not run network test unless in maintainer mode.</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">ifneq (1,$(DEB_MAINTAINER_MODE))</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">TEST_FILES := $(filter-out t/04_DB_TRANSFAC.t,$(shell echo t/*.t))</span>
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<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -2,11 +2,11 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>libtfbs-perl</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="shell"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></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="shell"></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<a href="https://salsa.debian.org/med-team/libtfbs-perl/-/compare/c5c5d21c72098ee87568bc16b553148807022c61...12f393b6900037f9dee9a7b68bed374bab49b15d#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS/issues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS/issues/new</span>
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1
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> - Author: Lenhard, Boris and Wasserman, Wyeth W.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics/18.8.1135</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" 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="12" 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">@@ -10,7 +12,8 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Pages: 1135-1136</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> Year: 2002</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> URL: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS.git</span>
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<td class="old_line diff-line-num old" data-linenumber="13" 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="LC13" class="line" lang="plaintext">Repository: http://www.ii.uib.no/svn/lenhard/TFBS/</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Repository: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS.git</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Repository-Browse: https://github.com/ComputationalRegulatoryGenomicsICL/TFBS</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> - Name: SciCrunch</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> Entry: SCR_015774</span>
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