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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mindthegap">Debian Med / mindthegap</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/13fe2c708489ada303b4d9aec3b4bf78adc661ee">13fe2c70</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-10T18:13:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">First stage of creating an additional "sub"package. Rectify mindthegap.install to prevent dh_missing from complaining
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<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/82e1d2d94e0493169f34dd4c9b105e0fafdeeca3">82e1d2d9</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-10T19:08:07Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling mistake & misc edit on mindthegap.install
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<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f">e24d2fa2</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-10T19:09:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create mindthegap-examples listing file src locations & their desired location
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#80e4eaa371fd96762163b4f21798615b8b94124c">
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+
debian/mindthegap-examples.install
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<li class="file-stats">
<a href="#994c38d628af0182d7d5e6a5b5a27ed310b621d1">
debian/mindthegap.install
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mindthegap/compare/bfc8320bb0306850eb39f5ef8bf4162aa119f1a3...e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,3 +29,22 @@ Description: Performs detection and assembly of DNA insertion variants in NGS re</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> tool. It can fill the gaps between a set of input contigs without any a</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> priori on their relative order and orientation. It outputs the results</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> in gfa file.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Package: mindthegap-examples</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> mindthegap</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Description: Optional scripts and example resources for mindthegap.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> Designed to call insertions of any size, whether they are novel or</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> duplicated, homozygous or heterozygous in the donor genome. it takes</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> as input a set of reads and a reference genome. It outputs two sets</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> of FASTA sequences: one is the set of breakpoints of detection</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> insertion sites, the other is the set of assembled insertions for</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> each breakpoint. MindTheGap can also be used as a genome assembly</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> finishing tool. It can fill the gap between a set of input contigs</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> without any a priori on their relative order and orientation. It</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> outputs the results in gfa file. Please note that this package is</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> meant to accommodate the mindthegap package and only acts as example</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> to how this package can be utilised.</span></pre>
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<a href="https://salsa.debian.org/med-team/mindthegap/compare/bfc8320bb0306850eb39f5ef8bf4162aa119f1a3...e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f#80e4eaa371fd96762163b4f21798615b8b94124c"><strong>debian/mindthegap-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">scripts</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">scripts</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vde</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"></span></pre>
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<a href="https://salsa.debian.org/med-team/mindthegap/compare/bfc8320bb0306850eb39f5ef8bf4162aa119f1a3...e24d2fa2bf1113a7984b53ffaae8dae384cb8c0f#994c38d628af0182d7d5e6a5b5a27ed310b621d1"><strong>debian/mindthegap.install</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">@@ -5,7 +5,6 @@ test/references usr/share/mindthegap/test</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">truths</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">sh</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">eval</span><span class="o" style="font-weight: 600;">.</span><span class="nx">cpp</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vde</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">fasta</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">info</span><span class="o" style="font-weight: 600;">.</span><span class="nx">txt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span><span class="o" style="font-weight: 600;">/*</span><span class="nx">gfa</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">contig_test</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,8 +14,7 @@ test/full_test/*.breakpoints usr/share/mindthegap/test/full_test</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">output</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span><span class="o" style="font-weight: 600;">/*.*.</span><span class="nx">vcf</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span><span class="o" style="font-weight: 600;">/</span><span class="nx">test</span><span class="o" style="font-weight: 600;">/</span><span class="nx">full_test</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="php"><span class="nx">data</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="php"><span class="nx">scripts</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="php"><span class="nx">CHANGELOG</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="php"><span class="nx">README</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mindthegap</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">MindTheGap</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="php"></span></pre>
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