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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lumpy-sv">Debian Med / lumpy-sv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/bc88ad19b7a7d2595d231b1865b45b695b2c18df">bc88ad19</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T21:10:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add own config file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/ce521e21dc25b9e9eb25bef48864e578d648da4f">ce521e21</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T21:22:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better description
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/186dabe6fd9147a62d557a96e80dcbafd4675f03">186dabe6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T21:22:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lumpy-sv/-/commit/2971fffc423487daf71caf3f94337c702d4996fb">2971fffc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-01T21:42:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add python3 to Build-Depends
</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#8d695f5062616d175c0a919bfe84431505824645">
<span class="new-file">
+
debian/etc/lumpyexpress.config
</span>
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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</li>
<li class="file-stats">
<a href="#6864ced7557ec33a7ee70c7b0c75b076f84f4fac">
debian/patches/lumpyexpress.config.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,6 +4,8 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new old_line" data-linenumber="7" 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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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libbamtools-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libfastahack-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libgzstream-dev,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="22" 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">@@ -20,6 +22,7 @@ Package: lumpy-sv</td>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ${python3:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> samblaster,</span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> samtools,</span>
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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> python3,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" 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="31" 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">@@ -28,8 +31,6 @@ Depends: ${shlibs:Depends},</td>
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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Recommends: sambamba</span>
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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Description: general probabilistic framework for structural variant discovery</span>
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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> LUMPY, a novel SV discovery framework that naturally integrates multiple</span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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="LC31" class="line" lang="plaintext"> SV signals jointly across multiple samples. We show that LUMPY yields</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> improved sensitivity, especially when SV signal is reduced owing to</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> either low coverage data or low intra-sample variant allele frequency.</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> We also report a set of 4,564 validated breakpoints from the NA12878</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> human genome.</span></pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> SV signals jointly across multiple samples. LUMPY yields improved</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> sensitivity, especially when SV signal is reduced owing to either low</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> coverage data or low intra-sample variant allele frequency.</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,20 +12,20 @@ Copyright: 2011-2014 Ryan M. Layer</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Files:</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right">*/utils/BamTools-Ancillary</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right">*/utils/BlockedIntervals</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> <span class="idiff left right">*/utils/VectorOps</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> <span class="idiff left right">*/utils/bedFile</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right">*/utils/bedFilePE</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right">*/utils/bedGraphFile</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> <span class="idiff left right">*/utils/chromsweep</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right">*/utils/fileType</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">*/utils/genomeFile</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> <span class="idiff left right">*/utils/lineFileUtilities</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> <span class="idiff left right">*/utils/sequenceUtilities</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> <span class="idiff left right">*/utils/stringUtilities</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> <span class="idiff left right">*/utils/tabFile</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right">src/utils/BamTools-Ancillary/*</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right">src/utils/BlockedIntervals/*</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> <span class="idiff left right">src/utils/Point/*</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> <span class="idiff left right">src/utils/VectorOps/*</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> <span class="idiff left right">src/utils/bedFile/*</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right">src/utils/bedFilePE/*</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <span class="idiff left right">src/utils/bedGraphFile/*</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> <span class="idiff left right">src/utils/chromsweep/*</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right">src/utils/fileType/*</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">src/utils/genomeFile/*</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> <span class="idiff left right">src/utils/lineFileUtilities/*</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> <span class="idiff left right">src/utils/sequenceUtilities/*</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> <span class="idiff left right">src/utils/stringUtilities/*</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> <span class="idiff left right">src/utils/tabFile/*</span></span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Copyright: 2009-2011 Aaron Quinlan</span>
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> 2010 - Assaf Gordon, CSHL</span>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">License: GPL-2</span>
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<li id="8d695f5062616d175c0a919bfe84431505824645">
<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb#8d695f5062616d175c0a919bfe84431505824645"><strong>debian/etc/lumpyexpress.config</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="conf"><span class="n" style="color: #333;">LUMPY_HOME</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">share</span>/<span class="n" style="color: #333;">lumpy</span>-<span class="n" style="color: #333;">sv</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="conf"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="conf"><span class="n" style="color: #333;">LUMPY</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">lumpy</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="conf"><span class="n" style="color: #333;">HEXDUMP</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">hexdump</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="conf"><span class="n" style="color: #333;">SAMBLASTER</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">samblaster</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="conf"><span class="n" style="color: #333;">SAMBAMBA</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">sambamba</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="conf"><span class="n" style="color: #333;">SAMTOOLS</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">samtools</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="conf"><span class="n" style="color: #333;">PYTHON</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">bin</span>/<span class="n" style="color: #333;">python3</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="conf"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="conf"><span class="n" style="color: #333;">PAIREND_DISTRO</span>=/<span class="n" style="color: #333;">usr</span>/<span class="n" style="color: #333;">share</span>/<span class="n" style="color: #333;">lumpy</span>-<span class="n" style="color: #333;">sv</span>/<span class="n" style="color: #333;">scripts</span>/<span class="n" style="color: #333;">pairend_distro</span>.<span class="n" style="color: #333;">py</span></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;">#BAMGROUPREADS=/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py</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;">#BAMFILTERRG=/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="conf"><span class="c" style="color: #998; font-style: italic;">#BAMLIBS=/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py</span></span></pre>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">bin</span>/lumpyexpress.config etc/lumpy</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">scripts usr/share/lumpy-sv</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">bin/lumpy usr/bin</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">bin/lumpy_filter usr/bin</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">bin/lumpyexpress usr/bin</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">debian/etc</span>/lumpyexpress.config etc/lumpy</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">scripts <span class="idiff left right"> </span>usr/share/lumpy-sv</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">bin/lumpy <span class="idiff left right"> </span>usr/bin</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bin/lumpy_filter <span class="idiff left right"> </span>usr/bin</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">bin/lumpyexpress <span class="idiff left right"> </span>usr/bin</span></pre>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb#6864ced7557ec33a7ee70c7b0c75b076f84f4fac"><strong>debian/patches/lumpyexpress.config.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 26 May 2020 15:07:58 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Adapt path<span class="idiff left right">e</span>s to Debian locations</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Adapt paths to Debian locations</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/scripts/lumpyexpress</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/scripts/lumpyexpress</span></span>
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<a href="https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -4,21 +4,11 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</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">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></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"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with python3</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,3 +23,6 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> dh_link /etc/$(DEB_SOURCE)/lumpyexpress.config /usr/share/$(DEB_SOURCE)/scripts/lumpyexpress.config</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">override_dh_python3:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> dh_python3 --shebang=/usr/bin/python3</span></pre>
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